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 = 54.32 α = 90
b = 80.97 β = 110.56
c = 58.22 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 -- 2014-04-25
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
2.2 50 99.6 0.129 -- 18.75 6.7 -- 23996 -- -- --
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)
2.2 2.24 99.7 0.566 -- -- 6.5 1191

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 2.2 46.137 -- 0.0 -- 23046 1910 95.37 -- 0.191 0.1866 0.239 --
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 2.1968 2.2517 -- 119 1329 0.2248 0.2814 -- 84.0
X Ray Diffraction 2.2517 2.3126 -- 122 1439 0.216 0.2439 -- 91.0
X Ray Diffraction 2.3126 2.3807 -- 147 1436 0.2171 0.2669 -- 92.0
X Ray Diffraction 2.3807 2.4575 -- 122 1488 0.1999 0.2818 -- 94.0
X Ray Diffraction 2.4575 2.5453 -- 135 1465 0.213 0.2722 -- 94.0
X Ray Diffraction 2.5453 2.6472 -- 144 1492 0.2129 0.3163 -- 94.0
X Ray Diffraction 2.6472 2.7677 -- 132 1487 0.2017 0.2811 -- 95.0
X Ray Diffraction 2.7677 2.9136 -- 134 1521 0.2112 0.2523 -- 96.0
X Ray Diffraction 2.9136 3.0961 -- 142 1571 0.1921 0.2723 -- 99.0
X Ray Diffraction 3.0961 3.3351 -- 150 1557 0.2045 0.2758 -- 99.0
X Ray Diffraction 3.3351 3.6706 -- 135 1578 0.1879 0.2508 -- 99.0
X Ray Diffraction 3.6706 4.2014 -- 142 1565 0.1601 0.2311 -- 98.0
X Ray Diffraction 4.2014 5.2921 -- 143 1591 0.158 0.1982 -- 100.0
X Ray Diffraction 5.2921 46.147 -- 143 1617 0.1837 0.193 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.8774
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.69
f_chiral_restr 0.025
f_plane_restr 0.003
f_bond_d 0.003
f_dihedral_angle_d 13.099
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3848
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 141

Software

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