X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 293.0
Details 0.3M Tris, 0.5mM Zinc Acetate, 425mM Sodium Citrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.09 α = 90
b = 78.09 β = 90
c = 78.09 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 -- 2016-12-16
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2

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
1.17 31.88 98.81 0.063 -- -- 8.9 -- 26219 -- -- 11.9675
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)
1.175 1.217 89.84 0.469 -- 3.88 -- --

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 1.17464 31.8816 -- 1.34757 -- 26218 1250 98.8054 -- 0.141608 0.140917 0.154946 --
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 1.1746 1.2217 -- 135 2509 0.178395 0.193458 -- 90.8591
X Ray Diffraction 1.2217 1.2773 -- 142 2773 0.150038 0.173411 -- 100.0
X Ray Diffraction 1.2773 1.3446 -- 129 2794 0.137868 0.156545 -- 99.388
X Ray Diffraction 1.3446 1.4289 -- 138 2779 0.117422 0.144337 -- 100.0
X Ray Diffraction 1.4289 1.5392 -- 144 2772 0.115829 0.147766 -- 99.6582
X Ray Diffraction 1.5392 1.6941 -- 161 2792 0.118491 0.129325 -- 99.831
X Ray Diffraction 1.6941 1.9392 -- 108 2829 0.129772 0.146648 -- 99.6269
X Ray Diffraction 1.9392 2.443 -- 125 2846 0.152457 0.146294 -- 100.0
X Ray Diffraction 2.443 31.8933 -- 168 2874 0.14709 0.163437 -- 99.7704
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.6374
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.00599849
f_chiral_restr 0.0739509
f_bond_d 0.0142123
f_dihedral_angle_d 14.9116
f_angle_d 1.373
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 398
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 72

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692+SVN
XDS data reduction
XDS data scaling
PHENIX phasing
PHENIX model building