X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 100 mM HEPES, pH 7.0, 0.7-0.8 M NaH2PO4, 0.75 M KH2PO4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.29 α = 90
b = 160.29 β = 90
c = 235.86 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-03-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792, 0.9197, 1.4586, 1.1398, 1.0718, 1.0087 APS 24-ID-E

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
3.01 200 99.19 0.08633 -- -- 7.7 -- 35894 -- -- 120.04
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)
3.01 3.1173 98.2 2.012 -- 0.66 7.6 --

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
MIRAS 3.01 80.15 -- 1.34 -- 35840 1792 99.18 -- 0.2222 0.2193 0.277 Random selection
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 3.01 3.09 -- 131 2534 0.3556 0.395 -- 97.76
X Ray Diffraction 3.09 3.18 -- 135 2552 0.3817 0.438 -- 99.81
X Ray Diffraction 3.18 3.28 -- 137 2602 0.3679 0.4518 -- 99.64
X Ray Diffraction 3.28 3.4 -- 136 2569 0.3094 0.3901 -- 99.63
X Ray Diffraction 3.4 3.54 -- 136 2579 0.2653 0.2855 -- 99.56
X Ray Diffraction 3.54 3.7 -- 137 2610 0.2276 0.3038 -- 99.53
X Ray Diffraction 3.7 3.89 -- 137 2595 0.218 0.2927 -- 99.64
X Ray Diffraction 3.89 4.14 -- 137 2606 0.193 0.2584 -- 99.46
X Ray Diffraction 4.14 4.46 -- 138 2629 0.1711 0.245 -- 99.25
X Ray Diffraction 4.46 4.91 -- 138 2615 0.166 0.235 -- 99.39
X Ray Diffraction 4.91 5.62 -- 139 2649 0.2012 0.2547 -- 99.15
X Ray Diffraction 5.62 7.08 -- 142 2683 0.2582 0.3051 -- 99.12
X Ray Diffraction 7.08 80.15 -- 149 2825 0.2098 0.2559 -- 97.67
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 148.17
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.0459
f_bond_d 0.004
f_dihedral_angle_d 4.4174
f_angle_d 0.7501
f_plane_restr 0.0047
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7247
Nucleic Acid Atoms 0
Heterogen Atoms 83
Solvent Atoms 28

Software

Software
Software Name Purpose
PHENIX refinement version: 1.15.2_3472
PHENIX refinement version: 1.15.2_3472
Coot model building version: 0.8.8
XDS data reduction
XDS data scaling
AutoSol phasing