Category em_3d_fitting
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
Example 1:
Example 1 - EMDB entry EM1078
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' .
Example 2:
Example 2 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
_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.
;
Key Category Items
Items in Category em_3d_fitting
