X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 289.0
Details 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.71 α = 90
b = 139.55 β = 124.97
c = 87.62 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2010-07-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID

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
2.32 34.23 99.4 -- 0.054 9.443 3.4 60715 60715 -- -- 50.48
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)
2.32 2.44 99.7 0.481 0.481 1.6 3.5 8864

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 2.32 34.226 -- 0.0 -- 60304 3077 99.39 -- 0.1987 0.1973 0.2249 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 2.32 2.38 -- 216 4245 0.2284 0.2723 -- 99.39
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.18
Anisotropic B[1][1] -7.6498
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.0377
Anisotropic B[2][2] 11.9502
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.3004
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 13.16
t_angle_deg 1.13
t_omega_torsion 2.63
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.294
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8986
Nucleic Acid Atoms 0
Heterogen Atoms 323
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.15
BUSTER-TNT refinement version: 2.9.3
PDB_EXTRACT data extraction version: 3.15
XDS data reduction