X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.15
Details 0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.32 α = 90
b = 107.61 β = 90
c = 263.85 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-11-16
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97894 SSRF BL17U

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
2.45 65.14 96.5 0.066 -- -- 6.5 -- 52753 -- -- 58.29
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)
2.45 2.54 -- 0.547 -- -- -- --

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 2.454 65.135 -- 1.34 -- 52683 2639 96.41 -- 0.2111 0.2087 0.2582 --
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 2.4541 2.4987 -- 164 2711 0.2951 0.3596 0.0 100.0
X Ray Diffraction 2.4987 2.5468 -- 163 2647 0.2865 0.3475 0.0 100.0
X Ray Diffraction 2.5468 2.5988 -- 162 2671 0.2791 0.3255 0.0 100.0
X Ray Diffraction 2.5988 2.6553 -- 127 2645 0.3097 0.3884 0.0 98.0
X Ray Diffraction 2.6553 2.7171 -- 77 1201 0.3237 0.4662 0.0 97.0
X Ray Diffraction 2.7171 2.785 -- 145 2690 0.2645 0.3476 0.0 100.0
X Ray Diffraction 2.785 2.8603 -- 125 2733 0.2599 0.3135 0.0 100.0
X Ray Diffraction 2.8603 2.9445 -- 138 2661 0.2654 0.3078 0.0 99.0
X Ray Diffraction 2.9445 3.0395 -- 153 2667 0.2643 0.3357 0.0 99.0
X Ray Diffraction 3.0395 3.1482 -- 130 2701 0.2622 0.335 0.0 98.0
X Ray Diffraction 3.1482 3.2742 -- 135 2725 0.2432 0.2642 0.0 100.0
X Ray Diffraction 3.2742 3.4232 -- 142 2711 0.229 0.3343 0.0 100.0
X Ray Diffraction 3.4232 3.6037 -- 126 2746 0.2273 0.2785 0.0 100.0
X Ray Diffraction 3.6037 3.8294 -- 142 2687 0.2313 0.2568 0.0 99.0
X Ray Diffraction 3.8294 4.1251 -- 143 2757 0.2002 0.2676 0.0 99.0
X Ray Diffraction 4.1251 4.5401 -- 130 2723 0.1696 0.2211 0.0 100.0
X Ray Diffraction 4.5401 5.1968 -- 149 2760 0.1656 0.1886 0.0 100.0
X Ray Diffraction 5.1968 6.5465 -- 161 2694 0.1938 0.2279 0.0 97.0
X Ray Diffraction 6.5465 65.1 -- 127 2914 0.1657 0.2041 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.9412
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_plane_restr 0.005
f_angle_d 0.704
f_chiral_restr 0.045
f_dihedral_angle_d 6.471
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9713
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 63

Software

Software
Software Name Purpose
PHENIX refinement version: 1.11.1_2575
AutoPROC data collection
AutoPROC data scaling
Coot model building
PHENIX phasing