X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 287.0
Details 0.1M imidazole, 0.2M sodium chloride, 30%(w/v) PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.09 α = 90
b = 133.09 β = 90
c = 227.11 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2012-05-19
Diffraction Radiation
Monochromator Protocol
Si double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPRING-8 BL26B1

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
2.8 50 88.8 -- -- -- -- -- 98528 18.3 45.0 --
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)
2.8 -- 88.8 -- -- -- -- --

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 2.9 19.93 -- -- 23686 23686 1202 91.9 0.28238 0.28238 0.28131 0.30235 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 2.9 2.974 -- 246 4506 0.381 0.38 -- 89.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.144
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.016
r_chiral_restr 0.197
r_dihedral_angle_4_deg 23.841
r_dihedral_angle_3_deg 28.687
r_dihedral_angle_2_deg 39.145
r_dihedral_angle_1_deg 12.411
r_angle_refined_deg 3.499
r_bond_refined_d 0.026
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5878
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 57

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
PHASES model building
HKL-2000 data collection