2XKX

Single particle analysis of PSD-95 in negative stain

ELECTRON MICROSCOPY - SOLUTION SCATTERING

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Solution Scattering Data Acquistion	1	2
Scattering Type	x-ray	modelling
Radiation/Neutron Source	SRS
Synchrotron	Y
Beamline Type	STATION 2.1
Detector Type	MULTIWIRE 2-D
Detector Manufacturer Details
Temperature (K)	277
pH
Numer of Time Frames Used	64
Protein Concentration Range (mg/mL)	1-8
Sample Buffer	20MM TRIS/HCL, 5MM DTT, 1MM EDTA, PH 7.5, 50MM NACL
Data Reduction Software	OTOKO/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
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 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 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 Type	GENERIC FILM
Electron Dose (electrons/Å**2)

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI 10
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2250
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)	0.1
Nominal CS	3.6
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	43000
Calibrated Magnification
Source	TUNGSTEN HAIRPIN
Acceleration Voltage (kV)	100
Imaging Details	LOW DOSE

EM Software
Task	Software Package	Version
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	EMAN

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	PARAMETERS DETERMINED USING SCATTERING CURVE