X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 291.15
Details 14-14.5% (w/v) PEG 3350 200mM sodium malonate pH 6.8-7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 185.07 α = 90
b = 185.07 β = 90
c = 185.07 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M-F -- 2014-04-29
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA

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
2.75 46.27 100.0 -- 0.09 -- 39.8 -- 27492 -- -- --
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)
2.75 2.82 100.0 -- -- 1.9 40.7 --

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
SIRAS 2.75 46.267 -- 1.37 -- 27492 1374 99.97 -- 0.2378 0.2369 0.2558 --
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 2.7503 2.8486 -- 137 2607 0.4061 0.4339 -- 100.0
X Ray Diffraction 2.8486 2.9626 -- 134 2561 0.3234 0.3817 -- 100.0
X Ray Diffraction 2.9626 3.0974 -- 137 2599 0.2967 0.3131 -- 100.0
X Ray Diffraction 3.0974 3.2607 -- 137 2598 0.2792 0.3169 -- 100.0
X Ray Diffraction 3.2607 3.4649 -- 136 2579 0.2709 0.3232 -- 100.0
X Ray Diffraction 3.4649 3.7324 -- 137 2605 0.2585 0.2844 -- 100.0
X Ray Diffraction 3.7324 4.1078 -- 138 2624 0.2343 0.2646 -- 100.0
X Ray Diffraction 4.1078 4.7017 -- 137 2612 0.2082 0.2137 -- 100.0
X Ray Diffraction 4.7017 5.9216 -- 139 2628 0.2201 0.2118 -- 100.0
X Ray Diffraction 5.9216 46.274 -- 142 2705 0.2167 0.242 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 109.036
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.662
f_bond_d 0.003
f_plane_restr 0.004
f_chiral_restr 0.024
f_dihedral_angle_d 10.98
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4436
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 13

Software

Software
Software Name Purpose
XSCALE data scaling
SHELXDE phasing
PHENIX refinement version: 1.9_1692
PDB_EXTRACT data extraction version: 3.20
XDS data reduction