Solution Scattering Data Analysis and Model Fitting
Method
Software
Software Authors
Starting Model
Conformers, Number Calculated
Conformers, Number Submitted
Conformers, Selection Criteria
Best Representative Conformer
Other Details
RIGID BODY MODELLING
SASREF7/BUNCH8
PETOUKHOV, M. V. & SVERGUN, D. I.
PROGRAM PRE-BUNCH 1IU0/1QLC/1TP5/1KJW + SEQUENCE DATA
20
2
TWO MAJOR CONFORMERS WERE PRESENT IN THE POOL OF REFINED SAXS MODELS CHAIN A REPRESENTS THE BEST AGREEMENT WITH THE EXPERIMENTAL SAXS DATA (CHI=3.3). CHAIN B IS REPRESENTATIVE OF THE SECOND CONFORMATION (CHI=3.8).
NUMBER OF TIME FRAMES USED 24 (60S, 4.25M CAMERA), 40(60S, 1M CAMERA). PROTEIN CONCENTRATION 1 MG/ML (4.25M CAMERA) 8 MG/ML (1M CAMERA)
Sample
RAT PSD-95
Specimen Preparation
Sample Aggregation State
PARTICLE
Staining Type
NEGATIVE
Staining Material
Uranyl Acetate
Staining Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
7854
Reported Resolution (Å)
22.9
Resolution Method
Other Details
THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELA ...
THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, THIS COMPOSITE STRUCTURE IS THEN FITTED INTO AN EM MAP. DOMAINS PROVIDED BY X-RAY, NMR POSITIONED BY BUNCH ( PETOUKHOV, M. V. & SVERGUN, D. I. (2005). GLOBAL RIGID BODY MODELING OF MACROMOLECULAR COMPLEXES AGAINST SMALL- ANGLE SCATTERING DATA. BIOPHYS J 89, 1237-50.) REFINEMENT SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1761. (DEPOSITION ID: 7384).
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (1IU0, 1QLC, 1TP5, 1KJW)
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION
MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE
...
METHOD--A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION
MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE
EXPERIMENTAL MAP BY MAXIMIZING THE CROSS-CORRELATION WITH THE EXPERIMENTAL MAP.
THE COORDINATES WERE THEN REPLACED IN THE CALCULATED MAP TO GENERATE THE FINAL
ENTRY. REFINEMENT PROTOCOL--DOCKED USING CHIMERA