X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 3.6M Naformate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 32.84 α = 90
b = 47 β = 90
c = 78.73 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-12-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979 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
1.52 30.31 97.8 0.186 -- -- -- 27637 19456 -- -3.0 21.413
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)
1.34 1.42 87.9 0.01 -- 0.87 -- --

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 1.52 30.309 -- 1.99 -- 19328 580 99.44 -- 0.2016 0.2011 0.2183 RANDOM
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 1.52 1.6729 -- 143 4610 0.2986 0.3172 -- 100.0
X Ray Diffraction 1.6729 1.9149 -- 144 4642 0.2281 0.2724 -- 100.0
X Ray Diffraction 1.9149 2.4125 -- 144 4663 0.1853 0.2137 -- 100.0
X Ray Diffraction 2.4125 30.315 -- 149 4833 0.1839 0.1886 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.1107
Anisotropic B[1][1] 17.6776
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.4225
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.2551
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.665
f_plane_restr 0.005
f_chiral_restr 0.064
f_angle_d 0.952
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1037
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 129

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction