X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS(pH6.5), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.42 α = 90
b = 77.42 β = 90
c = 38.04 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-27
Diffraction Radiation
Monochromator Protocol
Numerical type Si(111) double crystal monochromator, liquid nitrogen cooling SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 PHOTON FACTORY BL-17A

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
1.19 54.74 99.8 0.074 -- -- 13.8 -- 37127 -- -- --
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)
1.19 1.21 99.4 0.262 -- 10.3 12.0 21972

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 1.19 50.0 -- -- -- 35699 1877 99.86 -- 0.16823 0.16759 0.18037 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 1.19 1.221 -- 145 2574 0.148 0.164 -- 99.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.497
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.154
r_sphericity_free 3.283
r_rigid_bond_restr 0.894
r_bond_refined_d 0.007
r_angle_refined_deg 1.211
r_dihedral_angle_1_deg 5.637
r_dihedral_angle_2_deg 33.383
r_dihedral_angle_3_deg 12.379
r_dihedral_angle_4_deg 14.799
r_chiral_restr 0.093
r_gen_planes_refined 0.005
r_mcbond_it 0.82
r_mcangle_it 1.392
r_scbond_it 1.711
r_scangle_it 2.576
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 992
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 171

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
MOLREP model building
HKL-2000 data collection