2XKX | pdb_00002xkx

Single particle analysis of PSD-95 in negative stain


ELECTRON MICROSCOPY - SOLUTION SCATTERING

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IU0 
experimental modelPDB 1QLC 
experimental modelPDB 1TP5 
experimental modelPDB 1KJW 
Solution Scattering Data Acquistion12
Scattering Typex-raymodelling
Radiation/Neutron SourceSRS
SynchrotronY
Beamline TypeSTATION 2.1
Detector TypeMULTIWIRE 2-D
Detector Manufacturer Details
Temperature (K)277
pH
Numer of Time Frames Used64
Protein Concentration Range (mg/mL)1-8
Sample Buffer20MM TRIS/HCL, 5MM DTT, 1MM EDTA, PH 7.5, 50MM NACL
Data Reduction SoftwareOTOKO/GNOM
Guiner Mean Radius Of Gyration (nm)4.36
Sigma Mean Radius Of Gyration
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)14.0
Solution Scattering Data Analysis and Model Fitting
MethodSoftwareSoftware AuthorsStarting ModelConformers, Number CalculatedConformers, Number SubmittedConformers, Selection CriteriaBest Representative ConformerOther Details
RIGID BODY MODELLINGSASREF7/BUNCH8PETOUKHOV, M. V. & SVERGUN, D. I.PROGRAM PRE-BUNCH 1IU0/1QLC/1TP5/1KJW + SEQUENCE DATA202TWO 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 StatePARTICLE
Staining TypeNEGATIVE
Staining MaterialUranyl Acetate
Staining Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles7854
Reported Resolution (Å)22.9
Resolution Method
Other DetailsTHE 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 TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1IU0, 1QLC, 1TP5, 1KJW)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--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
Data Acquisition
Detector TypeGENERIC FILM
Electron Dose (electrons/Å**2)
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI 10
Minimum Defocus (nm)900
Maximum Defocus (nm)2250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)0.1
Nominal CS3.6
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification43000
Calibrated Magnification
SourceTUNGSTEN HAIRPIN
Acceleration Voltage (kV)100
Imaging DetailsLOW DOSE
EM Software
TaskSoftware PackageVersion
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONEMAN
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PARAMETERS DETERMINED USING SCATTERING CURVE