X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.6
Temperature 293.15
Details 15% PEG6000, 5% glycerol; Drop volume: 0.2ul; Protein proportion: 50%; Protein concentration: 6 mg/ml, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.14 α = 90
b = 61.85 β = 90
c = 139.06 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
PIXEL DECTRIS PILATUS 6M -- 2011-10-02
Diffraction Radiation
Monochromator Protocol
Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.127 PETRA III EMBL c/o DESY P13 (MX1)

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 61.85 96.9 0.113 -- -- 4.6 20020 19858 -- 3.0 24.44
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)
2.0 2.11 87.1 0.577 -- 2.5 3.1 --

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 2.01 37.09 -- 0.0 19706 19706 1004 96.68 0.2092 0.2092 0.2067 0.258 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 2.01 2.12 2614 144 2470 0.211 0.2625 -- 96.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.25
Anisotropic B[1][1] 0.0799
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4656
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.3857
RMS Deviations
Key Refinement Restraint Deviation
f_omega_torsion 2.68
f_other_torsion 2.95
f_angle_deg 0.97
f_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.325
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2582
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 150

Software

Software
Software Name Purpose
MxCuBE data collection
PHASER phasing
PHENIX refinement
BUSTER refinement version: 2.11.2
XDS data reduction
SCALA data scaling