Data items in the EM_2D_CRYSTAL category record details about the crystallographic cell parameters. Space-group number from International Tables for Crystallography, Vol. A (1987). Unit-cell angle alpha in degrees of the reported structure. Unit-cell angle beta in degrees of the reported structure. Unit-cell angle gamma in degrees of the reported structure. The cell settings for this space-group symmetry. A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c Unit-cell length a corresponding to the structure reported. Unit-cell length b corresponding to the structure reported. Unit-cell length c corresponding to the structure reported. Hermann-Mauguin space-group symbol. Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1987) and indicate the origin and the setting if it is not implicit. P 1 21/m 1 P 2/n 2/n 2/n (origin at -1) R -3 2/m This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_2D_CRYSTALS category record details for a 2D crystal experiment. General details on the filaments studied The value of attribute id in category em_2D_crystals must uniquely identify set of the filament parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - EMDB entry EM1078 <mmcif_iims:em_3d_fittingCategory> <mmcif_iims:em_3d_fitting id="1" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> <mmcif_iims:em_3d_fitting id="2" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> <mmcif_iims:em_3d_fitting id="3" entry_id="EM1078"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> </mmcif_iims:em_3d_fitting> </mmcif_iims:em_3d_fittingCategory> Example 2 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_3d_fittingCategory> <mmcif_iims:em_3d_fitting id="1" entry_id="1DYL"> <mmcif_iims:method>AUTOMATIC</mmcif_iims:method> <mmcif_iims:target_criteria>R-FACTOR</mmcif_iims:target_criteria> <mmcif_iims:ref_space>REAL</mmcif_iims:ref_space> <mmcif_iims:ref_protocol>RIGID BODY REFINEMENT</mmcif_iims:ref_protocol> <mmcif_iims:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. </mmcif_iims:details> </mmcif_iims:em_3d_fitting> </mmcif_iims:em_3d_fittingCategory> Any additional details regarding fitting of atomic coordinates into the 3d-em volume. partial Description of local variance of fit of the atomic coordinates into the 3dem volume map. The method used to fit atomic coordinates into the 3dem reconstructed map. The overall B (temperature factor) value for the 3d-em volume. Description of the quality of fit of the atomic coordinates into the 3dem volume map. The quality of fit of the atomic coordinates into the 3dem volume map. The type of protocol used in the refinement. rigid body A flag to indicate whether fitting was carried out in real or reciprocal refinement space. The quality of fit of the atomic coordinates into the 3dem volume map. best visual fit using the program O The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed volume map. This data item is a pointer to _entry_id in the ENTRY category. Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on EM entry 1078 The end sequence ID for the pdb entry chain used in the fitting The EM entry id pointer The chain id for the resulting fitted coordinates The PDB code for the entry produced by the fitting. Description of a particular component pdb entry used in fitting. The chain id for the entry used in fitting. The PDB code for the entry used in fitting. The symmetry required to be applied to the starting PDB entry chain before starting the fitting procedure The start sequence ID for the pdb entry chain used in the fitting The (1,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (1,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (2,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (3,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,1) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,2) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,3) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement The (4,4) element of a 4,4 matrix relating the starting PDB chain to the fitted coordinates in the case of rigid body refinement This data item is a unique identifier. The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_3d_reconstructionCategory> <mmcif_iims:em_3d_reconstruction entry_id="1DYL" id="1"> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> <mmcif_iims:resolution>9.</mmcif_iims:resolution> </mmcif_iims:em_3d_reconstruction> </mmcif_iims:em_3d_reconstructionCategory> The Amplitude correction method. Frequency amplitude correction with X-ray scattering data enhances the Fourier amplitudes of a reconstructed cryo-EM volume so they more closely resemble those of experimental low-angle X-ray scattering data. Normal amplitude correction (in which case the SNR weighted averaging of particles will still occur properly) may be applied or without it, in which case the (phase-flipped) data is not corrected during averaging, then the final 3D model is 'fixed'. This data item is a pointer to attribute id in category citation in the CITATION category. The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. CTF correction of each particle General details on the 3d recontruction Orientation determination using the random-conical data collection method. This method uses a defined geometry in the data collection, and is able to find the handedness of the structure unambiguously. Each specimen field is imaged twice, once tilted, once untilted. Particles are selected simultaneously from both untilted- and tilted-specimen fields, using a special interactive particle-selection program that is able to "predict" the location of a particle in the tilted-specimen field when its counterpart has been selected in the untilted field. From the untilted-specimen particle data set, all particles are selected that exhibit the same view. This can be done by using alignment followed by classification. The corresponding tilted-specimen data subset can be used to compute a reconstruction: the orientations of the tilted-particle projections lie on a cone with fixed angle (the tilt angle) and random azimuths (the in-plane angles found in the alignment of the untilted particle set). 1 Orientation determination using common lines (a.k.a. "angular reconstitution"). This method is based on the fact that in Fourier space any two projections intersect along a central line ("the common line"). Hence, in principle, the relative orientations between three projections can be determined - except that the handedness of the constellation is ambiguous. Because of the low signal-to-noise ratio of raw particle images, averages of projections falling into roughly the same orientation must be used. Since the procedure leads to solutions presenting local minima, it must be repeated several times to find solutions that form a cluster, presumably around the global minimum. Such clustering of solutions can be detected by multivariate statistical analysis of the resulting 3D maps. Two clusters are expected, one for each enantiomorph. After initial structure is obtained, it should be further refined using 3D projection matching strategy described next. 2 Orientation determination by 3D projection matching. Here the existing 3D map is projected in many orientations on a regular angular grid, and the resulting projections that are compared, one by one, with each of the experimental projections. This comparison (by cross-correlation ) yields a refined set of Eulerian angles , with which a refined reconstruction can be computed using one of the possible reconstruction techniques. This procedure requires iteration until the angles for each projection stabilize. 3 General details describing any local symmetry used in the single particle reconstruction The algorithm method used for the 3d-reconstruction. e.g. Random-conical reconstruction: a method of data collection and reconstruction used for single particles, typically used initially in a project, to obtain a first low-resolution reconstruction of the macromolecule [Radermacher et al., 1987]. Two images of the same specimen field are collected, one with untilted grid, the other with the grid tilted by 50 to 60 degrees. Any set of particles presenting the same view in the untilted-specimen image form a random-conical projection set in the associated tilted-specimen image. Helical reconstruction Helical reconstruction is used when the protein of interest forms a natural helix. Since the helix is a recurring structure with a very well defined pattern, the repeating pattern of the helix can be exploited to solve the structure. In this case, no alignment of the particles is needed, since the individual positions of subunits within the helix are clearly defined by the shape of the helix. Two common examples of structures solved by helical reconstruction are TMV and microtubules. Icosahedral reconstruction Icosahedral reconstructions also take advantage of internal symmetry and repetition to generate a detailed three-dimensional structure from the data set. In this case, the symmetry is icosahedral (twenty-one sided). Many viruses exhibit icosahedral symmetry in their capsid proteins, and this method has been used to solve their structures. Electron crystallography Electron crystallography is similar to x-ray crystallography in that it exploits the repeating pattern found within a crystal to generate a structure. Just as with x-ray crystallography, difraction patterns are generated and are used to define an electron density map. However, it differs in that the crystal used is a two-dimensional sheet as opposed to three three-dimensional crystals of x-ray crystallography. Common Lines Another reconstruction method searches for the intersection of any two projections in Fourier space. The Fourier transform of the experimental projections all form slices around a common core in Fourier space. Therefore, the intersection of these projections are unique (unless the projections perfectly overlap), and their relative orientation can be found when three or more projections are used. A principal problem with this method is that the handedness of the image is lost. This, however, can later be corrected by visual examination of the model with other known structural information. Back Projection As its name implies, back projection is the inverse function of projection. When an n-dimensional object is projected, each projection is an n-1 dimensional sum of its density along the projection axis. Therefore, a sphere would have circles as its projections. A cube, on the other hand, would produce either squares, diamonds, or other intermediate parallelograms depending on the direction of projection. The actual shape, of course, depends on the orientation from which the projection was made. The reverse function is called back projection and regenerates the original object. cross-common lines The number of asymmetric units used in the single particle reconstruction The number of particles used in the 3d reconstruction The final resolution (in angstroms)of the 3d reconstruction. The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off The actual pixel size of projection set of images in x IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. The actual pixel size of projection set of images in y IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. The actual pixel size of projection set of images in z IF only attribute voxel_size_x in category em_3d_reconstruction is given then a cube is assumed. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction. Data items in the EM_3D_REFINEMENT category record details about the class/particle refinement. In random conical tilt, images were assigned angular positions through rotational alignment and tilt-angles. From each different class, a three-dimensional preliminary model is constructed. To improve the output, those preliminary models from each class that have a high degree of similarity are merged. In theory, these models corresponded to groups of the same molecule just viewed from different orientations. Once all the good random conical tilt models (and their corresponding particle data sets) have been merged, iterative angular refinement is used to improve the model's resolution. Equidistant projections are first generated from the merged model. The entire particle data set (whether the old random conical tilt experimental particles, or new untilted experimental particles, or both) is then cross correlated to each reference projection. A correlation coefficient is generated between each experimental particle and reference projection. For each individual experimental particle, it is matched to the reference projection that gave the highest correlation coefficient. Therefore, it is assumed that this particle matches the Euler angles of the reference projection. Alignment radius (pixels) used in alignment search the angular_search_step_size used in refinement Convergence criterion fraction e.g. Converges when x16 % of all images move < 1.5 * stepsize This data item is a pointer to attribute id in category entry in the ENTRY category. the max_spatial_frequency used in refinement (1/A) Description of the 3d refinement method the number of iterations used in refinement the Projection radius in pixels the structure_radius in pixels The value of attribute id in category em_3d_refinement must uniquely identify the refinement used in the em experiments. Data items in the EM_ARRAY_FORMATION category record details of growth conditions for the array samples. Example 1 - based on PDB entry 1AT9 and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_array_formationCategory> <mmcif_iims:em_array_formation id="1" type="2D-CRYSTAL"> <mmcif_iims:atmosphere>room air</mmcif_iims:atmosphere> <mmcif_iims:pH>5.2</mmcif_iims:pH> <mmcif_iims:temp>18.</mmcif_iims:temp> <mmcif_iims:buffer_id>2</mmcif_iims:buffer_id> <mmcif_iims:details>on grid</mmcif_iims:details> <mmcif_iims:citation_id>2</mmcif_iims:citation_id> </mmcif_iims:em_array_formation> </mmcif_iims:em_array_formationCategory> The type of the apparatus used for growing the array. Langmuir trough The type of atmosphere in which arrays were grown. room air This data item is a pointer to attribute id in category em_solution_composition. This data item is a pointer to attribute id in category citation in the CITATION category. Any additional items concerning array growth. Two-dimensional Crystallization-- Purified protein (2 mg/ml) was mixed with E. coli lipids solubilized in OTG (mixed micelles stock solution, 4 mg/ml E. coli lipids in 20 mM Mes-NaOH (pH 6), 5% OTG, 0.01% NaN3) to achieve a lipid to protein ratio of 1 (w/w). The final protein concentration was adjusted to 1.33 mg/ml, and the final OTG content was adjusted to 1.93%. The reconstitution mixture (60 µl) was preincubated at room temperature for 30 min and dialyzed against 1.5 liters of 10 mM Mes-NaOH (pH 6), 100 mM NaCl, 100 mM MgCl2, 2 mM dithiothreitol, 0.01% NaN3 for 24 h at room temperature, 24 h at 37 °C, and another 24 h at room temperature. The method used for growing the array. lipid monolayer the pH value used for growing the array. 4.7 This data item is a pointer to attribute id in category em_solution_composition in the EM_SOLUTION_COMPOSITION category. The value of the temperature in degrees Kelvin used for growing the arrays. 293 The length of time required to grow the array. approximately 2 days The value of attribute id in category em_array_formation must uniquely identify the sample. The value of attribute type in category em_array_formation must identifies the type of array studied. Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_assemblyCategory> <mmcif_iims:em_assembly id="1" entry_id="1DYL"> <mmcif_iims:name>virus</mmcif_iims:name> <mmcif_iims:aggregation_state>icosahedral</mmcif_iims:aggregation_state> <mmcif_iims:composition>virus</mmcif_iims:composition> <mmcif_iims:num_components>1</mmcif_iims:num_components> </mmcif_iims:em_assembly> </mmcif_iims:em_assemblyCategory> A description of the aggregation state of the assembly. The known composition of the assembly. A description of any additional details describing the observed sample. This structure was preferentially oriented (end-on)on the grid. 1 The structure was monodisperse. 2 The name of the assembly of observed complexes. The number of components of the biological assembly. The author determined highest resolution of the reconstruction The author determined lowest resolution of the reconstruction The author determined resolution of the reconstruction The value of attribute id in category em_assembly must uniquely identify a collection of observed complexes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_CLASSES category record details about the particle classification. Particle classification involves grouping images that are similar, and separating images that are distinct. In practical use, this means that experimental projections that have the same orientation (shape) are placed within the same category for later averaging. In this case, orientation means that the particles are showing the same face to the viewer and the only difference between them is that they can be rotated by some angle in the plane of the image. The experimental projections might also be shifted relative to each other, but the centering of the experimental projections is often done before classification. is this required? E(e1,e2,e3) = E(w,h,i) cos(i)cos(h)cos(w)-sin(i)sin(h) cos(i)cos(h)sin(w)+sin(i)sin(h) -cos(i)sin(h) -sin(i)cos(h)cos(w)-cos(i)sin(h) sin(i)cos(h)sin(w)+cos(i)sin(h) sin(i)sin(h) sin(h)cos(w) sin(h)sin(w) cos(h) The alignment_method used The percentage angular error threshold The average_angular_error in degrees The average_translational_pixel_shift_error The clustering_method used Description of the classes derived in the em experiments. We have used size variation analyses to classify images recorded from preparations of the WT S. cerevisiae PDC to which sufficient E1 was added to occupy its 60 binding sites and the same preparation with about one-third of the E1 binding sites occupied. Two 3D reconstructions representative of images that vary in size by 10-12% (~50 Å in diameter) from these preparations were computed to document the E1 organization about the core and the length of its inner linkers. In this regard, our previous structure of the WT bovine kidney PDC in which ~22 E1s were bound indicated that the outer shell could readily accommodate 60 molecules of E1 without significant crowding. Surprisingly, this study shows that extensive E1 binding favors a more extended inner linker and an altered arrangement of E1 about the core. 1 The focal pair method of orientation determination, refinement, and 3D reconstruction as implemented in the IMIRS software package was used except that an additional step of particle-size evaluation was performed in the current reconstruction. Data sets consisting of 1,500 and 690 particle images of PDC with a molar ratio of 60 E1/E2 core and ~24 E1/E2 core, respectively, were processed. For both data sets, an iterative procedure was implemented to classify the particles according to their sizes by using the SIZEDIFF program with contrast transfer function correction incorporated. A preliminary 3D reconstruction was calculated by combining all of the particles, and this "average" reconstruction was used to classify the images into a 1.0 size group comprising a 3% size variation of the images. For the PDC with ~60 E1/E2 core, the converged structure from 128 images in the 1.0 size group, was then used as a model to classify 45 and 80 images in the 0.95 and 1.05 size groups, respectively. For the WT PDC preparation (24 E1/E2 core) the converged structure from 80 images in the 1.0 size group was used as model to classify 46 and 53 images in the 0.95 and 1.05 size groups, respectively. The image size distribution appears bell-shaped and is consistent with a more extensive data set of the human PDC (Y.G., Z.H.Z., Y. Hiromasa, H. Bao, X. Yan, T. E. Roche, and J.K.S., unpublished results). The finding that 1.0 size groups consist of the larger and smaller reconstructions in the PDC preparations according to their greater or lesser degree of E1 occupancy, respectively, indicates that the extent of E1 binding is related to the variable size of the molecules. 2 A classification was performed using the self-organizing map (SOM) algorithms of the XMIPP package. The entire set was first low pass-filtered to 3.2 nm, and a reference-free alignment was performed using the Spider software package. Transformations in x, y, and in-plane angle were imposed, and the data set was fed to the kernel density SOM procedure using a 10 x 10 grid. The procedure generates a grid of code vectors that represent the assigned images. It was verified that clean looking code vectors represented classes of clean particles, while particles assigned to defect-ridden code vectors were themselves of poor quality. The procedure was repeated several times with different parameters, and in each case a set of roughly 3000 good particles was obtained. Further processing was conducted on a set containing 2943 particles. 3 The picked particles were submitted to a multivariate statistical analysis without alignment and were classified into clusters of particles with similar features. To this end, a program package kindly provided by J. P. Bretaudière was used. The various cluster averages revealed square and round shaped particles at different angular orientations. These averages were taken as references for subsequent angular and translational alignment of the extracted 4096 particles. Aligned particles were classified again, and cluster averages were calculated. 4 This data item is a pointer to attribute id in category entry in the ENTRY category. The euler angle about z-axis The euler angle about y-axis The second euler angle about z-axis The fractional_minimum_amplitude The global_correlation_coefficient The global_real-space_correlation_coefficient flag for method used for internal resolution The number of particles used in the class average The class origin in X The class origin in Y The value of attribute id in category em_classes must uniquely identify the classes used in the em experiments. Data items in the EM_CRYO_STAIN category record details about the staining techniques used. Text describing a reference citation on the staining techniques used A mandatory flag to indicate if the data items describe cryo staining or not If the details given are for a cryogen staining method the name of the cryogen used General details on the staining techniques used The humidity at which the staining technique was used Details on the instrument used in the staining technique used Text describing the protocol for the staining techniques used A pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category The staining technique temperature used Text giving details on the time factors involved in the staining techniques used The general class or type of the staining technique used The value of attribute id in category em_cryo_stain must uniquely identify set of stain parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_detectorCategory> <mmcif_iims:em_detector entry_id="1DYL" id="1"> <mmcif_iims:type>KODAK SO163 FILM</mmcif_iims:type> </mmcif_iims:em_detector> </mmcif_iims:em_detectorCategory> The detector binning in x The detector binning in y Any additional information about the detection system. The detector dimension in x The detector dimension in y The exposure time in micro-seconds The exposure type Description of film_processing_conditions The detector offset in x from the top left corner of the CCD The detector offset in y from the top left corner of the CCD This data item is a pointer to attribute id in category entry in the ENTRY category. The detector pixel size The detector read-out speed The detector type used for recording images. Usually film or CCD camera. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_detector must uniquely identify the detector used for imaging. Data items in the EM_ELECTRON_DIFFRACTION category record details about the electron diffraction data from the electron crystallography experiment. Example 1 - based on PDB entry 1TUB and laboratory records for the structure corresponding to PDB entry 1TUB <mmcif_iims:em_electron_diffractionCategory> <mmcif_iims:em_electron_diffraction entry_id="1TUB" id="1"> <mmcif_iims:num_structure_factors>12000</mmcif_iims:num_structure_factors> <mmcif_iims:details xsi:nil="true" /> </mmcif_iims:em_electron_diffraction> </mmcif_iims:em_electron_diffractionCategory> Details of the electron diffraction experiment THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN INDUCED BY THE PRESENCE OF ZN++ IONS. WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY. GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE. 1 The number of diffraction patterns used from the electron diffraction experiment. The number of structure factors from the electron diffraction experiment. 12000 The value of attribute id in category electron_diffraction must uniquely identify the electron diffraction experiment. This data item is a pointer to attribute id in category entry in the ENTRY category. data items in the em_electron_diffraction_pattern category record details about the pattern information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <mmcif_iims:em_electron_diffraction_patternCategory> <mmcif_iims:em_electron_diffraction_pattern entry_id="1TUB" id="1"> <mmcif_iims:num_patterns_by_tilt_angle>1</mmcif_iims:num_patterns_by_tilt_angle> <mmcif_iims:num_images_by_tilt_angle>4</mmcif_iims:num_images_by_tilt_angle> </mmcif_iims:em_electron_diffraction_pattern> </mmcif_iims:em_electron_diffraction_patternCategory> the number of images by tilt angle. 4 the number of diffraction patterns by tilt angle. 1 the tilt angle at which the diffraction pattern was obtained. the value of attribute id in category electron_diffraction_pattern must uniquely identify the electron diffraction pattern experiment. this data item is a pointer to attribute id in category entry in the ENTRY category. data items in the em_electron_diffraction_phase category record details about the phase information from the electron diffraction experiment. example 1 - based on pdb entry 1tub and laboratory records for the structure corresponding to pdb entry 1tub <mmcif_iims:em_electron_diffraction_phaseCategory> <mmcif_iims:em_electron_diffraction_phase entry_id="1TUB" id="1"> <mmcif_iims:d_res_high>4.0</mmcif_iims:d_res_high> </mmcif_iims:em_electron_diffraction_phase> </mmcif_iims:em_electron_diffraction_phaseCategory> the highest resolution d-value for the electron diffraction experiment. 5.0 the highest resolution shell error in degrees. the overall phase error in degrees. the rejection criteria (phase error) in degrees. the phase residual value for the electron diffraction experiment. the value of attribute id in category electron_diffraction_phase must uniquely identify the electron diffraction phase experiment. this data item is a pointer to attribute id in category entry in the entry category. Data items in the EM_EMBEDDING_AGENT category record details about the type of reagents into which the sample was embedded Details on a reference citation on the embedding agent used General details on the embedding agent used The temperature the embedding agent was used at Details about the effect of time resolution for the embedding agent used The type of embedding agent used The value of attribute id in category em_embedding_agent must uniquely identify set of the embedding agent parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_entity_assemblyCategory> <mmcif_iims:em_entity_assembly id="1" assembly_id="1"> <mmcif_iims:type>VIRUS</mmcif_iims:type> </mmcif_iims:em_entity_assembly> </mmcif_iims:em_entity_assemblyCategory> Additional details about the component. The cell from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane A flag to indicate whether the component is engineered. The expression system used to produce the component. eschericia coli saccharomyces cerevisiae The plasmid used in the expression system used to produce the component. pBR322 pMB9 The organelle from which the component was obtained. golgi mitochondrion cytoskeleton The common name of the species of the natural organism from which the component was obtained. The species of the natural organism from which the component was obtained. The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the component was obtained. heart liver eye lens The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 The name of the component of the observed assembly. Alternative name of the component. FADV-1 A description of types of components of the assembly of the biological structure. The value of attribute id in category em_entity_assembly must uniquely identify each of the components of the complex. This data item is a pointer to attribute id in category em_assembly in the ASSEMBLY category. Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component. Example 1 - microtubule <mmcif_iims:em_entity_assembly_listCategory> <mmcif_iims:em_entity_assembly_list entity_assembly_id="1" id="1" entity_id="1"> <mmcif_iims:details>DIMER</mmcif_iims:details> <mmcif_iims:number_of_copies>2</mmcif_iims:number_of_copies> </mmcif_iims:em_entity_assembly_list> </mmcif_iims:em_entity_assembly_listCategory> The oligomeric state of the entity. The value (in megadaltons) of the molecular weight of each component of the assembly determined by attribute mol_wt_method in category em_entity_assembly_list. The method used in determining the molecular weight. Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80 °C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 ± 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. The number of copies of the entity. This data item is a pointer to attribute id in category em_entity_assembly in the ENTITY_ASSEMBLY category. The value of attribute id in category em_entity_assembly_list must uniquely identify the component. A pointer to entity id. Data items in the EM_ENTITY_ASSEMBLY_MOL_WT category record details of the molecular weight of structural elements in each component. Example 1 - microtubule <mmcif_iims:em_entity_assembly_mol_wtCategory> <mmcif_iims:em_entity_assembly_mol_wt id="1"> <mmcif_iims:mol_wt>12000.</mmcif_iims:mol_wt> <mmcif_iims:mol_wt_method>Calculated</mmcif_iims:mol_wt_method> </mmcif_iims:em_entity_assembly_mol_wt> </mmcif_iims:em_entity_assembly_mol_wtCategory> The value (in megadaltons) of the experimentally determined molecular weight of each component of the assembly. The method used in determining the molecular weight. Scanning Transmission Electron Microscopy Mass Measurement-- PM28 isoforms solubilized in OTG were adsorbed for 1 min to glow discharged thin carbon films supported by a thick fenestrated carbon layer (directly after cation-exchange chromatography). The gold-plated copper grids were then washed on 8 drops of quartz double-distilled water and were freeze-dried at -80 °C overnight in the microscope. For mass analysis, annular dark-field images were recorded in a STEM (VG-HB5) at 80 kV and doses of 325 ± 35 electrons/nm2. Digital acquisition of the images and microscope parameters, system calibration, and mass analysis were carried out as described previously. The total experimental error was calculated as the standard error of the mean, plus 5% of the measured particle mass to account for the absolute calibration uncertainty. The value of attribute id in category em_entity_assembly_mol_wt must uniquely identify the component. This is a pointer to attribute id in category em_entity_assembly_list. Data items in the EM_FILAMENTS category record details for a helical or filament type of experiment The axial rise per subunit of tubes used in the 3d reconstruction for the helical assembly. A description of the filament axial symmetry observed The value for delta Phi to describe the repeat parameters for a set of filaments The value for delta Z to describe the repeat parameters for a set of filaments General details on the filaments studied The value for the dyad to describe the repeat parameters for a set of filaments The helical family of tubes used in the 3d reconstruction for the helical assembly. The indices that characterise individual helical families are determined by the numbers of the two principal lines (helices) required to fill 360 degrees of azimuth. Each family of tubes gives rise to a distinct diffraction pattern determined by the number of principal 1,0 and 0,1 helical lines around the tube circumference and by the orientation of the surface lattice. Diffraction patterns from the images of the helical tubes consist of closely spaced lines of continuous intensity called layer-lines running perpendicular to the tube axis. Within a helical family of tubes the layer-line positions can also vary slightly, leading to a range of tube types characterised by a particular helical selection rule. The helical pitch of tubes used in the 3d reconstruction for the helical assembly. The subunits per helix turn of tubes used in the 3d reconstruction for the helical assembly. The value of attribute id in category em_filaments must uniquely identify set of the filament parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_FILAMENTS_RECONSTRUCTION category record details for the filamentary reconstruction The average phase residual for the helical assembly. Details on the method used for tilt and centering the helical axis. Correcting the layer line data for out-of-plane tilt, centering in the transform box, fitting to a reference data set and averaging was performed essentially as previously described [Milligan, R.A. and P.F Flicker. (1987) Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy. J. Cell Biol. 105 29-39 ]. Correction for tilt and centering require the user to specify amplitude peaks on certain strong layer lines which approximately match across the meridian. These peaks are determined computationally by identifying the amplitude maximum in the vector average of the near and far side of each layer line. The diameter of tubes used in the 3d reconstruction for the helical assembly. Details on how the high order layer lines were extracted The method described by Morgan, D.G., Owen, C., Melanson, L.A. and DeRosier, D.J. (1995) Structure of bacterial flagellar filaments at 11A resolution: Packing of the alpha helices. J. Mol. Biol. 249 88-110, was used by calculating a phase residual between each layer line in the average data set and a set of layer lines centered around the predicted layer line position for each individual filament. The layer line which results in the lowest phase residual is extracted to form a new average and the process is iterated. The layer-line resolution. Layer-lines fade out and are only visible to a certain resolution. Local symmetry details for the helical reconstruction. Pointer to the MAP_SYMMETRY category. The number of datasets used in the 3d reconstruction for the helical assembly. The number layer-lines used in the helical reconstruction. The number of sample points layer-line used in the helical reconstruction. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_FILAMENTS_SELECTION category record details for the selection of helical or filament particle types. The box criteria for tubes used in the 3d reconstruction for the helical assembly. For three-dimensional structure determination tubes are treated as helical objects and analysed by dividing them into axail repeat lengths, echa of which contains a complete set of views,e.g. The tube is first divided into (overlapping) portions, each corresponding to one axial repeat in length. Areas of tube boxed off from the digitised images and interpolated in real space so that after refinement an exact multiple of the axial repeat distance would be included in the Fourier transform. This means all the layer-lines fall exactly on the transform grid, while maintaining a constant sampling along the layer-lines so that different images can be easily compared. The whole repeats are boxed off and aligned against the reference dataset using Fourier terms extending only to the first or second zero in the CTF. Next the whole repeats are divided up into half-segments (length approximately equal to the radius of the tube), and the half segments are aligned against the reference data set. Finally the the segments themselves, in orientations determined from the half-segment alignment are refined against the reference dataset. Seven parameters are obtained for each segment: orientation in the image plane; out-of-plane tilt;effective repeat length; width relative to that of the reference;transverse, longitudinal and azimuthal alignments of the origin. The numeber of number of filaments_used used to refine the repeat parameters The numeber of unit cells or asymmetric units used to refine the repeat parameters Details on how located layer lines are used to choose a selection rule which best fits the data. Based on this selection rule the filament is then reboxed and restraightened using the original digitized image so that the final image contains an integral number of helical repeats. The selection rule define helical lattices which relate the layer- line number l to the order of the Bessel function, n, contributing to the layer-line. (n is the start number, ie number around the circumference, of the contributing helix). The diffraction pattern from a helix consists not of discrete spots but of difraction spots which have been broadened into layer-lines. The order of the Bessel functions allowed to contribute to the diffraction pattern of a helix on a given layer line versus the layer line along the ordinate gives a function which is described by a lattice. Such a plot is analogous to the diffraction pattern from a planar array corresponding to a flattened helix and is called an (n,l) plot. e.g. the n,l plot corresponding to the selection rule l = 5n + 12m where m is an integer and indicates e.g. 12 (ribosomes) per repeat five turns long, whilst the n,l plot corresponding to the selection rule l = 5n + 17m indicates 17(ribosomes) per repeat five turns along. Details on the method used to determine the path of the helical axis and thus correct curvature in the filaments. The filament axis was identified by first orienting the template to match the local orientation of a short segment of the original filament and then calculating a cross correlation between the reoriented template and this short segment of filament. This procedure is then repeated along the length of the filament. We have implemented such a procedure by having the user trace the approximate filament axis through identification a few points along the filament. A spline curve fitted to this axis provides the approximate local curvature of each filament segment. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_FSC_CURVE category record the values for the Fourier Shell Correlation Curve The x values in the FSC curve The y values in the FSC curve This data item uniquely identifies a row in the FSC curve attribute curve_id in category em_fsc uniquely identifies a fsc plot and is a pointer to attribute curve_id in category em_fsc in the EM_FSC category Data items in the EM_ICOS_VIRUS_SHELLS category record details of the viral shell number, diameter of each shell and triangulation number. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_icos_virus_shellsCategory> <mmcif_iims:em_icos_virus_shells virus_entity_id="1" id="1"> <mmcif_iims:shell_diameter>400.</mmcif_iims:shell_diameter> <mmcif_iims:triangulation_num>4</mmcif_iims:triangulation_num> </mmcif_iims:em_icos_virus_shells> </mmcif_iims:em_icos_virus_shellsCategory> The value of the diameter (in angstroms) for each protein shell of the virus. The triangulation number (T number) is a geometric and abstract concept that does not correspond to the structural components of an individul virus. It refers to the organisation of the geometric figure. The triangulation number, T is given by the following relationship: T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. 4 The value of attribute virus_entity_id in category em_icos_virus_shells is a pointer to attribute id in category em_virus_entity in the VIRUS_ENTITY category. The value of attribute id in category em_em_icos_virus_shells must uniquely identify the number and diameter of each virus protein shell and its triangulation number. Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_image_scansCategory> <mmcif_iims:em_image_scans entry_id="1DYL" id="2"> <mmcif_iims:scanner_model xsi:nil="true" /> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> </mmcif_iims:em_image_scans> </mmcif_iims:em_image_scansCategory> The number of bits per pixel. 8 This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details about scanning images. The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. 1.4 The scanner model. The spot size The sampling step size (microns) set on the scanner. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_image_scans must uniquely identify the images scanned. Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_imagingCategory> <mmcif_iims:em_imaging entry_id="1DYL" id="1"> <mmcif_iims:sample_support_id>1</mmcif_iims:sample_support_id> <mmcif_iims:microscope_id>1</mmcif_iims:microscope_id> <mmcif_iims:specimen_holder_model>gatan 626-0300</mmcif_iims:specimen_holder_model> <mmcif_iims:accelerating_voltage>200</mmcif_iims:accelerating_voltage> <mmcif_iims:illumination_mode>bright field</mmcif_iims:illumination_mode> <mmcif_iims:mode>low dose</mmcif_iims:mode> <mmcif_iims:nominal_cs>2.0</mmcif_iims:nominal_cs> <mmcif_iims:nominal_defocus_min>975.</mmcif_iims:nominal_defocus_min> <mmcif_iims:nominal_defocus_max>7600.</mmcif_iims:nominal_defocus_max> <mmcif_iims:tilt_angle_min>0.</mmcif_iims:tilt_angle_min> <mmcif_iims:tilt_angle_max>0.</mmcif_iims:tilt_angle_max> <mmcif_iims:nominal_magnification>50000</mmcif_iims:nominal_magnification> <mmcif_iims:electron_source>FEG</mmcif_iims:electron_source> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> <mmcif_iims:temperature>95.</mmcif_iims:temperature> </mmcif_iims:em_imaging> </mmcif_iims:em_imagingCategory> A value of accelerating voltage (in kV) used for imaging. 300 The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 This data item is a pointer to attribute id in category citation in the CITATION category. The condenser aperture used Any additional imaging details. Tilt series for tomographic reconstruction was recorded over a 124 degree angular range, using a 2 degree angular interval, with a high voltage electron microscope. Acceleration voltage = 1.0 MV. Em = AEI. Alignment using gold markers and cross-correlation. Reconstruction technique: Modified back-projection. Direction of missing wedge: 1 All image processing steps described below were performed using the Semper image processing system(Synoptics Ltd., Cambridge, United Kingdom). 2 The value of attribute detector_id in category em_imaging must uniquely identify the type of detector used in the experiment. The camera length (in millimetres). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. The electron dose received by the specimen (electrons per square angstrom). 0.9 The electron dose range received by the specimen (electrons per square angstrom). 0.9 - 1.1 The source of electrons. The electron gun. The type of energy filter spectrometer apparatus. FEI The energy filter range in electron volts (eV)set by spectrometer. 0 - 15 The mode of illumination. The imaging cryogen used A pointer to attribute id in category em_microscope in the EM_MICROSCOPE category The mode of imaging. The spherical aberration coefficient (Cs) in millimetres, of the objective lens. 1.4 The maximum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 7600 The minimum defocus value of the objective lens (in nanometres) used to obtain the recorded images. 975 The magnification indicated by the microscope readout. 60000 Description of the objective aperture used This data item is a pointer to attribute id in category entry in the ENTRY category. This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. The value of attribute scans_id in category em_imaging must uniquely identify the image_scans used in the experiment. Description of the selective aperture used The name of the model of specimen holder used during imaging. Description of the spot size used The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. The maximum angle at which the specimen was tilted to obtain recorded images. 60 The minimum angle at which the specimen was tilted to obtain recorded images. 0 This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_imaging must uniquely identify each imaging experiment. Data items in the EM_MAP category record details about the type of the 3d-em map. The map is represented logically as a three-dimensional array of data-values of the same data-type. To interpret the contents of of a 3d-map file it is necessary to know the data-type of the array and the size of the array in three dimensions (i.e.the number of columns, rows and sections). In a 1d-array representation columns are the fastest changing, followed by rows and sections. The first element of the array will have index 0. The 3d-em map is in a defined orientation/position in Universal 3D Space. This space is described by a right-handed cartesian coordinate system (and is the same coordinate system as that used for structures deposited in the PDB). Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_mapCategory> <mmcif_iims:em_map id="1" entry_id="EM9999"> <mmcif_iims:num_columns>100</mmcif_iims:num_columns> <mmcif_iims:num_rows>100</mmcif_iims:num_rows> <mmcif_iims:num_sections>100</mmcif_iims:num_sections> <mmcif_iims:value_density_max xsi:nil="true" /> <mmcif_iims:value_density_min xsi:nil="true" /> <mmcif_iims:value_density_mean xsi:nil="true" /> </mmcif_iims:em_map> </mmcif_iims:em_mapCategory> This data item is a pointer to the 2D_CRYSTAL_GROW category. This data item is a pointer to the 3D_RECONSTRUCTION category. The author_threshold for isosurface_countour_level for the map The map axis order fast The map axis order fast The map axis order slow Value of unit cell angle alpha in degrees. Value of unit cell angle beta in degrees. Value of unit cell angle gamma in degrees. Unit cell length a. Error standard deviation of unit cell length a. Unit cell length b. Error standard deviation of unit cell length b. Unit cell length c. Error standard deviation of unit cell length c. The limit in column size The contrast convention used for the map The map data_type describes the types of data in the map. Mode defines the data structure on disc. Mode 0=integer*1;mode 1=integer*2;mode 2=real*4. Mode 2 is the normal mode used in CCP4 programs. Any additional details about the map. Description of any enforced symmetry present in the map The method used to determine the hand of the virus. The hand is fixed for the reconstruction by combining the projections in a consistent way. Information gleaned from pairs of images of tilted particles must be used to validate a particular choice of hand. This data item is a pointer to the IMAGING category. The isosurface_countour_level for the map Description of any local symmetry present in the map Pointer to the MAP_EIGENVALUES category. This data item is a pointer to the MAP_FILES category. This data item is a pointer to the MAP_STRUCTURE_FACTORS category. This data item is a pointer to the EM_SYMMETRY category. The number of atoms. The number of class averages (one class average contains images that are the same) resulting from the multivariate statistical analysis of the individual images of particles are 2d projections of a 3d structure in different projection directions. Given a sufficiently large number of good 2d projections the 3d structure can be reconstructed knowing the orientational relationship between all the projection class averages. For an entirely asymmetric particle at least three different projections are required to solve the orientation problem. The number of columns of the map. The number of observations. The number of rows of the map. The number of sections of the map. The number of unique electron reflections collected. The x origin of the map. The y origin of the map. The z origin of the map. The percentage of possible reflections collected to specified resolution. The method used to determine the phase origin of the virus map. The x pixel size The y pixel size The z pixel size Description of any plane group present The R-free statistic value measures the agreement between the atomic model and the diffraction data for a 'test' set of reflections (usually 10%) that is omitted during refinement. The R-factor value compares overall agreement between the amplitudes of two sets of structure factors as follows: R= sigma || Fobs | - | Fcalc || / sigma | Fobs | For each reflection the magnitude of the computed difference between the observed structure-factor amplitude from the native data set |Fobs| and the calculated amplitude from the model in its current trial location |Fcalc| is summed for all reflections and divided by the sum of the observed structure factors. Wavelength of electrons in angstroms. Date (YYYY-MM-DD) of map release 2001-05-08 The limit in row size The limit in section size The space group number for the map The length of the x interval in microns. The length of the y interval in microns. The length of the z interval in microns. for 2d crystals the thickness Maximum density value in the map. Mean (average) density value of the map. Minimum density value in the map. The standard deviation density value of the map. Unique identifier of the volume map. This data item is a pointer to the ENTRY category. Data items in the EM_MAP_CTF_CORRECTION category record details about the CTF correction method. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL Any additional details about ctf correction. The method used to correct for the image distortions introduced by the phase contrast transfer function (CTF). CTF correction could be applied to the entire scanned micrograph or alternatively they may be applied to the extracted images of individual particles or at the end of the analysis to the density map reconstructed from the micrograph. Unique identifier for CTF correction of the map. This data item is a pointer to the EM_MAP category. Data items in the EM_MAP_EIGENVALUES category record details about values of the eigenvectors for projection sets. 2d projection images are considered as a linear combination of the main eigenvectors 'eigenimages' of the projection set, enabling a reduction of the total amount of data and simplifying its interpretation. The eigenvalue spectrum gives an indication of the randomness of the data that is included in the reconstruction. The completeness of the data can be verified eg all eigenvalues exceeded 1.0. Example 1 - Any additional details about the eigenvalues. The maximum eigenvalue. A low inverse eigenvalue indicates that many, well-spaced samples have been averaged to generate the coefficient while a high one indicates that only a few sample points were used so that the coefficient is more susceptible to noise. The minimum eigenvalue. A low inverse eigenvalue indicates that many, well-spaced samples have been averaged to generate the coefficient while a high one indicates that only a few sample points were used so that the coefficient is more susceptible to noise. A description of the eigenvalue spectrum for the data set used in the 3d reconstruction for the map. A data set consisting of pure noise has a characteristic eigenvalue spectrum which depends on the number of images, the number of image elements and the noise statistics. Since the eigenvalues are only determined by the spacing and number of the sample points, the eigenvalue spectrum is not affected by the signal to noise in the data or the reliability of the orientations. This information is seen from the resolution dependence of the phase residual seen during refinement. For the eigenvectors to be significant, the associated eigenvalues should stand out from the noise eigenvalue spectrum. Unique identifier of the EIGENVALUES category. This data item is a pointer to the EM_MAP category. Data items in the EM_MAP_FIGURE record details about figures associated with the map. These can consist of figures with associated text which are related to the map. Example 1 - Any additional details about the figure uploaded with the map. These could include captions. Unique identifier of the figure assembly. The number of bytes in the image file. Unique identifier of the figure assembly. This data item is a pointer to the EM_MAP category. Data items in the EM_MAP_FILES category record details about files relating to the map. These files can be uploaded and include files containing information about Example 1 - Any additional details about the files. The orthogonal slices x_slice file identifier. The orthogonal slices y_slice file identifier. The orthogonal slices z_slice file identifier. Unique identifier of the MAP_FILES category. This data item is a pointer to the EM_MAP category. Data items in the EM_MAP_RESOLUTION category record details about the Fourier Shell Correlation The most popular method at the moment for resolution assessment is the Fourier Shell Correlation, although there is no standard way to define the cutoff value. It assumes a uniform distribution of the resolution along the three-dimensions (so there is a single value of resolution). The Fourier Shell Correlation curve is defined as a list of value pairs (x, y) where x is the spatial frequency (or inverse resolution in 1/A) and y is the correlation coefficient (a value between 0 and 1). Example 1 <mmcif_iims:em_map_resolutionCategory> <mmcif_iims:em_map_resolution entry_id="EM9999"> <mmcif_iims:title>ACh receptor FSC Plot</mmcif_iims:title> <mmcif_iims:x_axis>Resolution (A-1)</mmcif_iims:x_axis> <mmcif_iims:y_axis>Correlation Coefficient</mmcif_iims:y_axis> </mmcif_iims:em_map_resolution> </mmcif_iims:em_map_resolutionCategory> Method used to determine the resolution of the map. The first of the two fundamentally different methods is one that relies on dividing the the data into two halves and then calculating two independent reconstructions which are then compared by Fourier Shell Correlation (FSC) or differential phase residual (DPR). The second different method of assessing resolution is more relevant where there is a combination of EM and X-ray data. The similarity between the EM density and the electron density corresponding to the atomic structure can be used to determine the resolution of the EM map. attribute curve_id in category em_map_resolution uniquely identifies a fsc plot The cutoff value to estimate the resolution value can be defined by: - the point of the curve where the correlation is 0.5 - the point of the curve that crosses a significance threshold curve According to Orlova et al. 1997 (J Mol Biol, 271:417) this significance threshold curve is defined as the 3*sigma (sigma = standard deviation of the FSC) for non-symmetrical particles. (units: 1/A) [stc stands for significance threshold curve] Any additional details about the resolution determination method. The value of the differential phase residual criterion. The two dimensional differential phase residual spatial frequency value. The differential phase residual value. The value of the fourier shell correlation criterion. A more accurate measure of the resolution is obtained by multiplying the sigma threshold value by the square root of the number of asymmetric units within the given point group symmetry. Reference: (Orlova et al, J mol Biol, 271, 417-437,1997). The fourier shell correlation significance threshold in sigma. e.g. a 3 sigma threshold is three standard deviations over the random noise value. The fourier shell correlation spatial frequency value. _em_map_resolution.map_id is a pointer to _em_map.id in the EM_MAP category The Nyquist frequency is double the sampling step. e.g. for data sampled at 5 angstroms the Nyquist frequency is 1/10 angstroms. It is important to have the sampling rate of the data high enough so that the image information stays sufficiently away from the Nyquist frequency, otherwise there is a danger that the high- resolution information in both of the reconstruction volumes may be correlated. The cut-off criteria used in the resolution determination.e.g an FSC limit of 0.5 is used as a conservative measure of resolution. the curve has to be weigthed taking into the account the number of independent asymmetric units (N). In that case the curve would be defined as sqrt(N)*3*sigma. This is the weighted factor used. If this weighted factor is always defined as 3*sqrt(N) then we only need to know the number of independent units N. The spectral-signal-to-noise ratio value. This two-dimensional resolution determination method compares reprojections. The title of the FSC graph - equivalent to the name of the assembly of observed complexes. The title of the x_axis in the FSC graph Usually the resolution in reciprical Angstroms may be spatial_frequency The title of the y_axis in the FSC graph The Correlation coefficient or sigma_value This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_MAP_STRUCTURE_FACTORS category record details about structure factors relating to the map. These are uploaded in a file. Example 1 - Any additional details about the structure factors file. Pointer to the MAP_FILES category. A description of how the structure factors of the masked cryo-EM maps were calculated. For example structure factors could be calculated by Fourier transformation using the progrma SFALL of the CCP4 package. Unique identifier of the map structure factors. This data item is a pointer to the MAP category. Data items in the EM_MAP_SURFACE_RENDERING category record details about surface rendering of the map. The surface of the map has to be defined and 'rendered' to make understandable images. The quality of the structure can be judged visually by looking at the high-resolution texture of the molecular surface. It can make sense to threshold/interpret data to 100% (or up to 120%) of the expected volume of the molecular assembly which has been calculated from the molecular mass. To emphasize the fine structures in the map thresholding values as little as 25% may be used. Example 1 - Any additional details about the surface rendered image. This data item is a pointer to the EM_FILES category. The method used to obtain the surface rendered image. The threshold volume molecular weight (as a percentage) used to produce the surface rendered image. Unique identifier of the surface rendered image figure of the assembly. This data item is a pointer to the EM_MAP category. Data items in the EM_MAP_SYMMETRY category record details about the symmetry of the assembly in the map. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_map_symmetryCategory> <mmcif_iims:em_map_symmetry map_id="1"></mmcif_iims:em_map_symmetry> </mmcif_iims:em_map_symmetryCategory> This is the enforced symmetry applied to the map. This is an equivalent xyz position. Unique identifier of the map symmetry. This is the plane group described using Herman Maugin nomenclature. This data item is a pointer the MAP category. Data items in the EM_MICROGRAPHS category record details about em raw data images The amplitude contrast e.g. 0.06 Astigmatism(axial): an electron-optical lens aberration that causes the defocus to be a function of azimuth, and the contrast transfer function to deviate from circular symmetry about the optical axis. As a consequence, the Thon rings deform into elliptic or hyperbolic patterns, depending on the size of defocus and the size of the astigmatic defocus difference. A flag for Y or N for astigmatism estimation The astigmatism ratio e.g. 0.96 For each micrograph smaller images are cropped from the image with the power spectrum found for all small images and they are averaged to improve signal to noise ratio. A flag for Y or N for circular averaging The difference between the two is that in Phase only correction only the phase of the CTF is flipped whereas in Phase and Amplitude correction, Wiener filtering is done to correct both phase and amplitude. If the envelope function and noise spectrum parameters are not available then phase only correction is recommended. For example if the parameters calculated from far from focus images are used to correct near to focus images (after adjusting for the defocus difference), the envelope function and noise spectrum parameter estimates of far from focus images are not reliable for near to focus images. The threshold set for edge detection for carbon and ice images. parameters of the CTF used for correcting are estimated from each image or parameters estimated for the far from images are used to correct near to focus images after compensating for the defocus Field size refers to the width of each small image cropped. An attribute averaging_overlap in category em_micrographs implies that the successive images have an overalp of (1-_em_micrographs.averaging_overlap)*field size. A higher value of attribute averaging_overlap in category em_micrographs means a greater number of smaller images are used for averaging. If the signal to noise ratio is very low, the averaging overlap should be changed for better estimate of power spectrum. The type of image filter used This data item is a pointer to attribute id in category em_microscope in the EM_MICROSCOPE category. The nominal defocus e.g. 2.00 The upper cutoff frequency The refined defocus estimate e.g. 1.975 This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. The value of attribute image_id in category em_micrograph must uniquely identify an image used in the em experiments. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_MICROSCOPE category record details about the microscope The microscope model The value of attribute id in category em_microscope must uniquely identify a microscope used in the em experiments. Data items in the EM_ORTHOGONAL_SLICES category record details about orthogonal slices through the map. These consist of an x-slice, y-slice and z-slice through the map. Example 1 - <mmcif_iims:em_orthogonal_slicesCategory> <mmcif_iims:em_orthogonal_slices> <mmcif_iims:id>1</mmcif_iims:id> </mmcif_iims:em_orthogonal_slices> </mmcif_iims:em_orthogonal_slicesCategory> This data item is a unique identifier for the ORTHOGONAL_SLICES category. The orthogonal x slice id. The orthogonal x slice number. The orthogonal y slice id. The orthogonal y slice number. The orthogonal z slice id. The orthogonal z slice number. This data item is a pointer to the MAP category. Data items in the EM_PARTICLE_LIST category record details about the picked particles 3d volume of the particle The particle alignment rotation in phi in the micrograph The particle alignment shift in X in the micrograph The particle alignment shift in Y in the micrograph The method for calculating similarities used to determine the [x,y,f] parameters. The correlation can be done either between images in the data set (CC) or by comparing an image to itself (AC). This data item is a pointer to attribute id in category entry in the ENTRY category. interpolation factor of the particle Y or N a noise image used to normalize the images as per histogram Y or N windowed particle template peak separation distance of the particle (its size) phi rotational alignment on the untilted-specimen images tilt_untilted_pairs angles between the two micrographs theta the tilt angle gamma angle between the tilt axis and the image y-axis in the untilted micrograph phi angle between the tilt axis and the image y-axis in the tilted micrograph The particle pixel X origin in the micrograph The particle pixel Y origin in the micrograph psi rotational alignment on the untilted-specimen images tilt_untilted_pairs angles between the two micrographs theta the tilt angle gamma angle between the tilt axis and the image y-axis in the untilted micrograph phi angle between the tilt axis and the image y-axis in the tilted micrograph The particle radius in the micrograph Y or N if used theta rotational alignment on the untilted-specimen images tilt_untilted_pairs angles between the two micrographs theta the tilt angle gamma angle between the tilt axis and the image y-axis in the untilted micrograph phi angle between the tilt axis and the image y-axis in the tilted micrograph A flag for Y or N for particles used in 3d reconstruction refinement Data items in the EM_PARTICLE_PICKING category record details about the method to pick particles from the raw micrographs The particle picking centering method The so-called center of gravity method where the image is scanned and the intensity peaks calculated to find the center of the particle 'mass'. The image is then shifted by the correct amounts to maximize the number of peaks near the center. Another centering method averages all the picked particles together, and then cross correlates each individual particle to the average. The cross correlation function is used to determine by how much to shift each particle when trying to center it. When all the particles have been cross correlated to the average and shifted, a new average is generated. Once again, all the particles are compared to the new average, and shifted as necessary to center them as best as possible. This iterative process is repeated until no significant shift is necessary for all the particles Crosscorrelating to a global average is but one variation on this theme. Similar methods also use an external model or a rotational average of the particle itself as the centering reference. Unfortunately, it can be difficult to obtain a reasonable external refernce, so a global average or a rotational average are most often used. Description of the reference citation on the method used Maxima having correlation scores below this threshold are not considered as possible particle locations. General details on the particle picking method Particles were picked using a program written in-house for selecting filaments. Lines are drawn over the filaments using the computer mouse, and the program selects coordinates for boxing the particles at a user-selected interval while keeping track of groups of particles coming from the same filament. This is useful where polarity can be determined per filament by two-dimensional averaging. The program also keeps track of the angle of the overlaid, user-drawn line, which is used for preliminary vertical orientation of the particles. 8440 particles of 80 x 80 pixel size were selected from the filaments. 1 A reference was established by selecting a well preserved particle and symmetrizing it 20-fold rotationally. Cross-correlation functions of this reference with images of digitized micrographs containing adsorbed particles of PM28 revealed correlation peaks at the particle positions, irrespective of their angular orientation. Using this particle picking method a gallery of 4096 particles was created. 2 Minimum difference between a peak and its surrounding trough in the correlation score. Radius used to test if a point's correlation score is locally maximal. Maximium radius of the peaks in the correlation score. The particle picking method Minimum radius of the peaks in the correlation score. Description of the pre-processing filters used This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_PARTICLE_PICKING_LIST category record details about the picked particles The value of attribute id in category em_particle_picking_list must uniquely identify a particle. This data item is a pointer to attribute id in category em_class in the EM_CLASS category. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to loading onto grid support. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_sample_preparationCategory> <mmcif_iims:em_sample_preparation entry_id="1DYL" id="1"> <mmcif_iims:ph>7.6</mmcif_iims:ph> <mmcif_iims:solution_id>1</mmcif_iims:solution_id> <mmcif_iims:sample_concentration>5.</mmcif_iims:sample_concentration> </mmcif_iims:em_sample_preparation> </mmcif_iims:em_sample_preparationCategory> This data item is a pointer to attribute id in category em_array_formation in the ARRAY_FORMATION category. Details on the sample preparation Selectively stained by injection of horseradish peroxidase, embedded in Spurr's resin and cut into 2-3 um thick sections. 1 Enzyme Preparations. S. cerevisiae PDC was purified to near homogeneity from baker's yeast by modification of a published procedure. Highly purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3 followed by FPLC on a Superdex 200 column. The weight-average molecular weight of the PDC was determined by light scattering measurement to be ~8 × 106. On the basis of the known molecular weight of the complex and its component enzymes and the experimentally determined polypeptide chain ratios of E2/BP/E3, we estimated that the subunit composition of the S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers, and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC preparation to increase the molar ratio of E1/E2 core to 60:1. This product is designated larger PDC or ~60 E1/E2 core PDC 2 embedment in vitreous ice. 3 Detergent-solubilized particles eluted from the cation-exchange column were directly adsorbed for 1 min to parlodion carbon-coated copper grids rendered hydrophilic by glow discharge at low pressure in air. Grids were washed with 4 drops of double-distilled water and stained with 2 drops of 0.75% uranyl formate. Images were recorded on Eastman Kodak Co. SO-163 sheet film with a Hitachi H-7000 electron microscope operated at 100 kV. Electron micrographs of single particles adsorbed to the carbon film were digitized using a Leafscan-45 scanner (Leaf Systems, Inc., Westborough, MA). 4 This data item is a pointer to attribute id in category entry in the ENTRY category. The pH value of the observed sample buffer. The value of the concentration (mg/mL for mg per milliliter) of the complex in the sample. This data item is a pointer to attribute id in category em_solution_composition in the EM_SOLUTION_COMPOSITION category. This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. The value of attribute id in category em_sample_preparation must uniquely identify the sample preparation. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_sample_supportCategory> <mmcif_iims:em_sample_support id="1"> <mmcif_iims:film_material>HOLEY CARBON</mmcif_iims:film_material> <mmcif_iims:grid_material>COPPER</mmcif_iims:grid_material> <mmcif_iims:grid_mesh_size>400</mmcif_iims:grid_mesh_size> <mmcif_iims:grid_type>MESH</mmcif_iims:grid_type> <mmcif_iims:pretreatment>GLOW DISCHARGE</mmcif_iims:pretreatment> <mmcif_iims:citation_id>2</mmcif_iims:citation_id> </mmcif_iims:em_sample_support> </mmcif_iims:em_sample_supportCategory> This data item is a pointer to attribute id in category citation in the CITATION category. A description of any additional details concerning the sample support. This grid plus sample was kept at -170 deg C for a month before use 1 A 3-µl sample of each PDC preparation (~0.35 mg/ml containing 20 µg/ml bacitracin) was deposited, blotted, and quick-frozen in liquid ethane on a glow-discharged carbon-coated holey grid. The vitrified samples were recorded at ~1 µm under focus at ~10 e/Å2 dose for image processing. A second exposure of ~2-3 µm under focus was recorded and used as an aid in analyzing the images with the focal pair method. The images were recorded on Kodak SO 163 film at a nominal magnification of ×50,000 in a JEOL JEM 1200 electron microscope operated at 100 kV. 2 Orientation of 4300 Ribosome projections identified by 3D projection matching using low resolution reference. (Penczek et al., 1994). Reconstruction (SIRT) simultaneously performed CTF correction (Zhu et al. submitted). 3 The support material covering the em grid. The name of the material from which the grid is made. The value of the mesh size (per inch) of the em grid. 400 A description of the grid type. A description of the method used to produce the support film. 1%formvar in chloroform cast on distilled water A description of the grid plus support film pretreatment. glow-discharged for 30 sec in argon The value of attribute id in category em_sample_support must uniquely identify the sample support. Data items in the EM_SINGLE_PARTICLES category record details for a sigle particle type of experiment General details describing the single particle The number of single particles used in the reconstruction The point group symmetry of the single particle The value of attribute id in category em_single_particles must uniquely identify set of the single particle parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the EM_SINGLEPARTICLE_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_singleparticle_selectionCategory> <mmcif_iims:em_singleparticle_selection entry_id="1"> <mmcif_iims:method>INTERACTIVE</mmcif_iims:method> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> </mmcif_iims:em_singleparticle_selection> </mmcif_iims:em_singleparticle_selectionCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details used for selecting observed assemblies. negative monitor contrast facilitated particle picking The method used for selecting observed assemblies. particles picked interactively from monitor The number of micrographs used The number of particles selected from the projection set of images. 840 The protocol used for selecting observed assemblies. The value of attribute entry_id in category em_singleparticle_selection points to the ENTRY category. Data items in the EM_SOLUTION_COMPOSITION category record details of the sample buffer. Any additional details to do with buffer. aerated The name of the buffer. Acetic acid The pH of the buffer. 6.93 The value of attribute id in category em_solution_composition must uniquely identify the sample solution conditions. Data items in the EM_STAIN category record details about the staining techniques used. Text describing a reference citation on the staining techniques used A mandatory flag to indicate if the data items describe cryo staining or not If the details given are for a cryogen staining method the name of the cryogen used General details on the staining techniques used The humidity at which the staining technique was used Details on the instrument used in the staining technique used Text describing the protocol for the staining techniques used A pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category The staining technique temperature used Text giving details on the time factors involved in the staining techniques used The general class or type of the staining technique used The value of attribute id in category em_stain must uniquely identify set of stain parameters This data item is a pointer to attribute id in category entry in the ENTRY category. Electron tomography allows the structural organisation of individual cells and organelles and bacterial cells to be studied at nanometre resolution. The samples are unique objects which precludes averaging over many copies so that tomograms are built from images of a tilt series taken from a single copy of the object. the StagePosition in X the StagePosition in Y General details on the tomographic experiment This data item is a pointer to attribute id in category entry in the ENTRY category. Number of sections used in reconstruction of tomographic map. Tilt angle increment in (degrees) used in reconstruction of tomographic map. The value of attribute id in category em_tomography must uniquely identify a collection of observed complexes. Data items in the EM_TOMOGRAPHY_IMAGE category record details of each of the images collected The defocus used for each image The electron_dose used for each image This data item is a pointer to attribute id in category entry in the ENTRY category. The exposure_time used for each image The magnification used for each image The pixel_size used for each image The shift in x used for each image The shift in y used for each image The tilt_angle used for each image The value of attribute id in category em_tomography_image must uniquely identify each tilted image Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_virus_entityCategory> <mmcif_iims:em_virus_entity id="1" entity_assembly_id="1"> <mmcif_iims:virus_host_category>VERTERBRATES</mmcif_iims:virus_host_category> <mmcif_iims:virus_host_species>HOMO SAPIENS</mmcif_iims:virus_host_species> <mmcif_iims:virus_type>VIRUS</mmcif_iims:virus_type> <mmcif_iims:virus_isolate>STRAIN</mmcif_iims:virus_isolate> <mmcif_iims:ictvdb_id>00.073.0.01.023</mmcif_iims:ictvdb_id> <mmcif_iims:enveloped>YES</mmcif_iims:enveloped> <mmcif_iims:empty>NO</mmcif_iims:empty> </mmcif_iims:em_virus_entity> </mmcif_iims:em_virus_entityCategory> Flag to indicate if the virus is empty or not. Flag to indicate if the virus is enveloped or not. The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. 01.0.2.0.001 01.0.2.0.002 The host category description for the virus. The host cell from which the virus was isolated. HELA CHO The host species from which the virus was isolated. homo sapiens gallus gallus The isolate from which the virus was obtained. The type of virus. Is the unique identifier for VIRUS_ENTITY category. This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <mmcif_iims:em_vitrificationCategory> <mmcif_iims:em_vitrification entry_id="1DYL" id="1"> <mmcif_iims:sample_preparation_id>1</mmcif_iims:sample_preparation_id> <mmcif_iims:cryogen_name>ETHANE</mmcif_iims:cryogen_name> <mmcif_iims:humidity>90</mmcif_iims:humidity> <mmcif_iims:temp>95.</mmcif_iims:temp> <mmcif_iims:protocol>PLUNGE VITRIFICATION</mmcif_iims:protocol> <mmcif_iims:citation_id>1</mmcif_iims:citation_id> <mmcif_iims:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER. </mmcif_iims:details> </mmcif_iims:em_vitrification> </mmcif_iims:em_vitrificationCategory> This data item is a pointer to attribute id in category citation in the CITATION category. This is the name of the cryogen. Any additional details relating to vitrification. argon atmosphere The humidity (%) in the vicinity of the vitrification process. 90 The type of instrument used in the vitrification process. The procedure for vitrification. blot for 2 seconds before plunging This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. The temperature (in degrees Kelvin) at which vitrification took place. 4.2 The length of time after an event effecting the sample that vitrification was induced and a description of the event. 30 msec after spraying with effector' The value of attribute id in category em_vitrification must uniquely identify the vitrification procedure. This data item is a pointer to attribute id in category entry in the ENTRY category.