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 = 55.63 α = 90
b = 81.53 β = 110.93
c = 58.98 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
1.9 50 97.2 0.064 -- 35.253 6.7 -- 37387 -- -- --
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)
1.9 1.93 99.1 0.71 -- -- 6.6 1891

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 1.905 40.797 -- 0.0 -- 35010 1889 90.91 -- 0.1928 0.1897 0.2455 --
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 1.9047 1.9562 -- 129 2253 0.2841 0.3211 -- 82.0
X Ray Diffraction 1.9562 2.0137 -- 132 2288 0.2546 0.2727 -- 82.0
X Ray Diffraction 2.0137 2.0787 -- 144 2391 0.2347 0.2766 -- 86.0
X Ray Diffraction 2.0787 2.153 -- 144 2481 0.2199 0.3067 -- 89.0
X Ray Diffraction 2.153 2.2392 -- 127 2444 0.2119 0.3021 -- 87.0
X Ray Diffraction 2.2392 2.3411 -- 145 2615 0.2065 0.2944 -- 94.0
X Ray Diffraction 2.3411 2.4645 -- 159 2692 0.1996 0.2602 -- 96.0
X Ray Diffraction 2.4645 2.6189 -- 154 2676 0.2012 0.267 -- 96.0
X Ray Diffraction 2.6189 2.8211 -- 151 2724 0.2008 0.2314 -- 97.0
X Ray Diffraction 2.8211 3.1049 -- 161 2736 0.2052 0.2844 -- 98.0
X Ray Diffraction 3.1049 3.554 -- 155 2643 0.209 0.257 -- 95.0
X Ray Diffraction 3.554 4.4767 -- 133 2486 0.1677 0.2398 -- 87.0
X Ray Diffraction 4.4767 40.8065 -- 155 2692 0.1617 0.2016 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.6801
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_chiral_restr 0.041
f_plane_restr 0.004
f_angle_d 1.052
f_dihedral_angle_d 14.511
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3709
Nucleic Acid Atoms 0
Heterogen Atoms 99
Solvent Atoms 139

Software

Software
Software Name Purpose
HKL-2000 data scaling
PHENIX refinement version: 1.9_1690
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction
PHENIX phasing