X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 292.0
Details 0.1 M HEPES, 0.2 M sodium citrate tribasic dihydrate, 13% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.98 α = 90
b = 77.98 β = 90
c = 77.98 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 6M-F -- 2014-10-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
1.5 50 100.0 0.065 -- 56.116 19.5 -- 12858 -- -- 19.62
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)
1.5 1.53 100.0 0.677 -- -- 19.1 617

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 1.5 27.57 -- 1.38 -- 12858 1295 100.0 -- 0.1461 0.1427 0.1766 --
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 1.498 1.5579 -- 143 1272 0.1215 0.1817 -- 100.0
X Ray Diffraction 1.5579 1.6288 -- 140 1269 0.1174 0.1497 -- 100.0
X Ray Diffraction 1.6288 1.7147 -- 135 1267 0.1118 0.1663 -- 100.0
X Ray Diffraction 1.7147 1.8221 -- 144 1286 0.1083 0.1724 -- 100.0
X Ray Diffraction 1.8221 1.9628 -- 145 1259 0.1182 0.154 -- 100.0
X Ray Diffraction 1.9628 2.1602 -- 147 1284 0.1193 0.1461 -- 100.0
X Ray Diffraction 2.1602 2.4726 -- 138 1284 0.1369 0.1794 -- 100.0
X Ray Diffraction 2.4726 3.1146 -- 145 1298 0.1477 0.1665 -- 100.0
X Ray Diffraction 3.1146 27.5751 -- 158 1344 0.1651 0.199 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.0461
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_angle_d 1.029
f_chiral_restr 0.09
f_dihedral_angle_d 10.26
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 404
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 48

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15