X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.2M magnesium chloride, 50.0% polyethylene glycol 200, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.34 α = 90
b = 118.74 β = 90
c = 239.87 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2012-08-02
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

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
2.9 46.83 98.8 0.146 -- -- -- -- 25634 -- -3.0 67.253
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)
2.9 3.0 94.7 0.738 -- 2.6 -- --

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
SAD 2.9 46.829 -- 0.0 -- 25634 1299 98.95 -- 0.1967 0.195 0.2288 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 2.9 3.02 -- 116 2619 0.2553 0.3076 -- 98.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.9052
Anisotropic B[1][1] -8.6126
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.9967
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.6093
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 3.01
t_omega_torsion 2.91
t_angle_deg 0.94
t_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.387
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4798
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 149

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: March 15, 2012
BUSTER-TNT refinement version: 2.10.0
XDS data reduction
SHELXD phasing
BUSTER refinement version: 2.10.0