X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.53 α = 90
b = 75.1 β = 110.72
c = 57.63 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.000 SSRL BL11-1

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
2.1 50 98.0 0.106 -- -- 6.7 -- 23908 -- -- --
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)
2.1 2.14 98.4 0.749 -- -- 6.1 --

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 2.1 45.12 -- 0.0 -- 22510 1885 92.1 -- 0.215 0.212 0.241 --
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 2.1028 2.1597 -- 118 1340 0.276 0.2933 -- 78.0
X Ray Diffraction 2.1597 2.2232 -- 132 1462 0.2589 0.3188 -- 85.0
X Ray Diffraction 2.2232 2.295 -- 145 1513 0.254 0.2936 -- 89.0
X Ray Diffraction 2.295 2.377 -- 142 1552 0.2417 0.2911 -- 91.0
X Ray Diffraction 2.377 2.4722 -- 147 1583 0.2425 0.2954 -- 92.0
X Ray Diffraction 2.4722 2.5847 -- 147 1611 0.2318 0.2981 -- 94.0
X Ray Diffraction 2.5847 2.7209 -- 145 1609 0.2365 0.255 -- 94.0
X Ray Diffraction 2.7209 2.8914 -- 145 1599 0.227 0.2728 -- 93.0
X Ray Diffraction 2.8914 3.1145 -- 150 1676 0.2275 0.2612 -- 97.0
X Ray Diffraction 3.1145 3.4279 -- 155 1676 0.2155 0.2426 -- 98.0
X Ray Diffraction 3.4279 3.9237 -- 156 1696 0.1911 0.1951 -- 98.0
X Ray Diffraction 3.9237 4.9424 -- 148 1626 0.1777 0.1922 -- 94.0
X Ray Diffraction 4.9424 45.1264 -- 155 1682 0.2008 0.2402 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.68
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.025
f_dihedral_angle_d 14.663
f_bond_d 0.003
f_plane_restr 0.003
f_angle_d 0.744
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3678
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 143

Software

Software
Software Name Purpose
PHENIX refinement
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHENIX phasing