X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.2 α = 90
b = 66.85 β = 93.81
c = 64.83 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2012-05-24
Diffraction Radiation
Monochromator Protocol
Si(111) channel cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 1.0781 NSLS X6A

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
1.66 27.79 99.6 -- 0.052 -- 5.2 38789 38789 -- -- --
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)
1.66 1.7 99.7 0.733 0.733 1.1 5.1 2884

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 1.66 27.79 -- 1.36 -- 38789 1905 99.63 -- 0.1922 0.1907 0.221 --
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 1.66 1.7015 -- 156 2615 0.2576 0.311 -- 100.0
X Ray Diffraction 1.7015 1.7475 -- 132 2619 0.2501 0.3143 -- 99.0
X Ray Diffraction 1.7475 1.7989 -- 126 2627 0.238 0.3178 -- 99.0
X Ray Diffraction 1.7989 1.857 -- 123 2622 0.2208 0.2414 -- 100.0
X Ray Diffraction 1.857 1.9233 -- 142 2620 0.2112 0.2364 -- 100.0
X Ray Diffraction 1.9233 2.0003 -- 148 2590 0.2003 0.2743 -- 100.0
X Ray Diffraction 2.0003 2.0913 -- 121 2661 0.1998 0.2098 -- 100.0
X Ray Diffraction 2.0913 2.2015 -- 129 2624 0.1837 0.2165 -- 100.0
X Ray Diffraction 2.2015 2.3394 -- 152 2640 0.1834 0.2111 -- 100.0
X Ray Diffraction 2.3394 2.5199 -- 139 2626 0.1945 0.2291 -- 100.0
X Ray Diffraction 2.5199 2.7733 -- 131 2646 0.1949 0.2441 -- 100.0
X Ray Diffraction 2.7733 3.1741 -- 118 2682 0.1901 0.2052 -- 100.0
X Ray Diffraction 3.1741 3.9972 -- 142 2657 0.1659 0.224 -- 100.0
X Ray Diffraction 3.9972 27.7935 -- 146 2655 0.1865 0.1837 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.7742
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.937
f_plane_restr 0.005
f_chiral_restr 0.079
f_angle_d 1.161
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1941
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 156

Software

Computing
Computing Package Purpose
SCALA Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.20 data reduction