X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 1.0 M sodium acetate trihydrate, 0.1 M HEPES, 0.05 M Cd(SO4) hydrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.78 α = 90
b = 92.78 β = 90
c = 95.71 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2013-10-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID

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
1.95 47.86 100.0 0.079 -- -- 12.9 -- 31128 -- -- 34.99
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)
1.95 2.0 100.0 1.771 -- -- 13.2 --

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 1.95 33.309 -- 1.92 -- 58073 2853 99.79 -- 0.1865 0.1852 0.2116 --
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 1.95 1.9836 -- 133 2783 0.2912 0.3131 -- 100.0
X Ray Diffraction 1.9836 2.0197 -- 115 2788 0.2754 0.2905 -- 100.0
X Ray Diffraction 2.0197 2.0586 -- 129 2755 0.2629 0.3081 -- 99.0
X Ray Diffraction 2.0586 2.1006 -- 132 2708 0.25 0.2796 -- 99.0
X Ray Diffraction 2.1006 2.1462 -- 167 2747 0.2398 0.3245 -- 100.0
X Ray Diffraction 2.1462 2.1961 -- 161 2723 0.2297 0.2823 -- 100.0
X Ray Diffraction 2.1961 2.2511 -- 130 2791 0.2037 0.2673 -- 100.0
X Ray Diffraction 2.2511 2.3119 -- 144 2759 0.2042 0.2219 -- 100.0
X Ray Diffraction 2.3119 2.3799 -- 173 2769 0.2025 0.2662 -- 100.0
X Ray Diffraction 2.3799 2.4567 -- 144 2733 0.1929 0.2054 -- 100.0
X Ray Diffraction 2.4567 2.5445 -- 151 2734 0.1919 0.1952 -- 100.0
X Ray Diffraction 2.5445 2.6463 -- 135 2791 0.1896 0.2098 -- 100.0
X Ray Diffraction 2.6463 2.7667 -- 170 2736 0.192 0.2269 -- 100.0
X Ray Diffraction 2.7667 2.9125 -- 165 2760 0.1909 0.2324 -- 100.0
X Ray Diffraction 2.9125 3.0948 -- 133 2780 0.1935 0.1946 -- 100.0
X Ray Diffraction 3.0948 3.3336 -- 112 2778 0.1846 0.279 -- 100.0
X Ray Diffraction 3.3336 3.6687 -- 102 2827 0.1899 0.1788 -- 100.0
X Ray Diffraction 3.6687 4.1987 -- 156 2743 0.1594 0.2013 -- 100.0
X Ray Diffraction 4.1987 5.2865 -- 138 2768 0.1422 0.1538 -- 100.0
X Ray Diffraction 5.2865 33.3143 -- 163 2747 0.18 0.1905 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.7509
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_dihedral_angle_d 9.91
f_angle_d 1.14
f_bond_d 0.01
f_chiral_restr 0.058
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1284
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 72

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.21
PHASER phasing version: 2.5.2
PHENIX refinement
PDB_EXTRACT data extraction version: 3.20
XDS data reduction