X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details reservoir: 100 mM sodium cacodylate, 15% glycerol, 10.5% PEG8000, 500 mM (NH4)2(SO4). drop: 0.002 ml reservoir solution, 0.002 ml 16 mg/ml protein in 20 mM Tris/HCl, pH 7.5, 5 mM MgCl2, 1 mM AMP-PNP, 1 mM NaN3, 0.0005 ml 1.0 M guanidinium chloride, 0.001 ml C12E8 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 201.78 α = 90
b = 201.78 β = 90
c = 171.63 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH MIRROR 1999-06-15
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
4 20 95.8 0.105 10.5 -- 6.0 224179 32750 -- -- 50.4
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
4.0 4.07 96.5 0.337 33.7 -- 3.2 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 4.0 15.0 -- 0.0 -- 32369 1611 95.8 -- 0.229 0.229 0.285 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 4.0 4.25 -- 280 5066 0.28 0.328 0.02 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.4
Anisotropic B[1][1] -6.06
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.11
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.004
x_angle_deg 0.9
x_scbond_it 11.97
x_mcbond_it 4.28
x_scangle_it 15.49
x_dihedral_angle_d 27.0
x_improper_angle_d 0.49
x_mcangle_it 6.67
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.55
Luzzati Sigma A (R-Free Set) 0.85
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12864
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 0

Software

Software
Software Name Purpose
AMoRE phasing
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling