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 = 76.82 α = 90
b = 76.82 β = 90
c = 38.08 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 link 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 54.32 100.0 0.096 -- -- 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 99.9 0.26 -- 10.6 12.3 22214

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 -- -- -- 35221 1851 99.96 -- 0.16472 0.16428 0.1732 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 -- 130 2553 0.151 0.186 -- 99.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.551
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.859
r_sphericity_free 3.353
r_rigid_bond_restr 0.891
r_bond_refined_d 0.007
r_angle_refined_deg 1.228
r_dihedral_angle_1_deg 5.541
r_dihedral_angle_2_deg 35.301
r_dihedral_angle_3_deg 11.325
r_dihedral_angle_4_deg 13.826
r_chiral_restr 0.091
r_gen_planes_refined 0.006
r_mcbond_it 0.793
r_mcangle_it 1.322
r_scbond_it 1.726
r_scangle_it 2.64
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 992
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 148

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