X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 291.0
Details 100 mM Tri-Na citrate, 0.2M MgCl2, 8% PEG3350 , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.52 α = 90
b = 98.52 β = 90
c = 90.01 γ = 120
Symmetry
Space Group P 3 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU -- 2011-07-20
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE Cu FINE FOCUS 1.5418 -- --

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
2.75 50 99.8 0.087 -- -- 9.8 13177 13151 0.0 0.0 53.39
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)
2.75 2.8 64.7 0.522 -- 1.55 9.7 647

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
FOURIER SYNTHESIS 2.75 24.042 0.0 1.35 13151 13149 1331 99.93 -- 0.1977 0.1893 0.2713 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 2.7503 2.8484 -- 134 1170 0.2876 0.3743 -- 100.0
X Ray Diffraction 2.8484 2.9623 -- 134 1179 0.2694 0.3633 -- 100.0
X Ray Diffraction 2.9623 3.0968 -- 133 1169 0.2319 0.3356 -- 100.0
X Ray Diffraction 3.0968 3.2597 -- 127 1170 0.2201 0.3448 -- 100.0
X Ray Diffraction 3.2597 3.4634 -- 129 1165 0.2165 0.2907 -- 100.0
X Ray Diffraction 3.4634 3.7299 -- 132 1186 0.1953 0.2883 -- 100.0
X Ray Diffraction 3.7299 4.1036 -- 128 1189 0.1765 0.2679 -- 100.0
X Ray Diffraction 4.1036 4.6936 -- 138 1180 0.1436 0.222 -- 100.0
X Ray Diffraction 4.6936 5.8989 -- 131 1183 0.1723 0.2252 -- 100.0
X Ray Diffraction 5.8989 24.0431 -- 145 1227 0.1689 0.2451 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.4288
Anisotropic B[1][1] 0.8429
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.8429
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6859
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.434
f_plane_restr 0.004
f_chiral_restr 0.074
f_angle_d 1.188
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3227
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 34

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction