Data Category em_3d_fitting

General

Category name
em_3d_fitting
Required in PDB entries
no
Category group membership
em_group  em_structure_analysis_group
Used in current PDB entries
Yes, in about 1.2 % of entries

Category Relationship Diagrams

70
View full category relationship diagram including all dictionary data categories
70
View abbreviated category relationship diagram including only those categories used in current PDB entries.

Category Description

     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

Category Examples

2

 
  loop_
   _em_3d_fitting.id                      
   _em_3d_fitting.entry_id               
   _em_3d_fitting.method    
   _em_3d_fitting.target_criteria  
   _em_3d_fitting.over_all_b_value       
   _em_3d_fitting.ref_space 
   _em_3d_fitting.ref_protocol            
   _em_3d_fitting.details                 
     1 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' .
     2 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' .
     3 EM1078 AUTOMATIC . . REAL 'RIGID BODY REFINEMENT' .
  
   _em_3d_fitting.id                      1
   _em_3d_fitting.entry_id                1DYL
   _em_3d_fitting.method                  AUTOMATIC
   _em_3d_fitting.target_criteria         R-FACTOR
   _em_3d_fitting.over_all_b_value        .
   _em_3d_fitting.ref_space               REAL
   _em_3d_fitting.ref_protocol            'RIGID BODY REFINEMENT'
   _em_3d_fitting.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.                                 
   ;