X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 148.77 α = 90
b = 158.05 β = 92.54
c = 254.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2011-10-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU

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
7 33.27 99.1 0.265 -- -- 3.782 -- 18745 -- -3.0 220.99
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)
7.0 7.41 98.2 1.146 -- 1.54 3.777 --

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 6.996 33.267 -- 1.35 -- 18619 1869 99.5 -- 0.3372 0.3375 0.3351 --
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 6.9965 7.1838 -- 143 1230 0.423 0.3964 0.0 96.0
X Ray Diffraction 7.1838 7.3929 -- 137 1291 0.4038 0.3978 0.0 100.0
X Ray Diffraction 7.3929 7.6288 -- 141 1262 0.3849 0.3948 0.0 100.0
X Ray Diffraction 7.6288 7.8979 -- 136 1314 0.3679 0.3921 0.0 100.0
X Ray Diffraction 7.8979 8.2096 -- 140 1275 0.3548 0.3993 0.0 100.0
X Ray Diffraction 8.2096 8.5772 -- 157 1260 0.3339 0.2996 0.0 100.0
X Ray Diffraction 8.5772 9.0208 -- 144 1301 0.333 0.3176 0.0 100.0
X Ray Diffraction 9.0208 9.5733 -- 135 1287 0.3153 0.2847 0.0 100.0
X Ray Diffraction 9.5733 10.2922 -- 151 1304 0.3 0.3124 0.0 100.0
X Ray Diffraction 10.2922 11.291 -- 145 1295 0.2832 0.2776 0.0 100.0
X Ray Diffraction 11.291 12.8418 -- 145 1282 0.2829 0.2895 0.0 99.0
X Ray Diffraction 12.8418 15.8808 -- 146 1323 0.3169 0.31 0.0 100.0
X Ray Diffraction 15.8808 33.2675 -- 149 1326 0.4085 0.4156 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 261.886
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.819
f_bond_d 0.014
f_plane_restr 0.008
f_dihedral_angle_d 19.218
f_chiral_restr 0.52
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 56599
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: dev_2614
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing