X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 1.2 M sodium citrate, 0.1 M HEPES-NaOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.55 α = 90
b = 87.55 β = 90
c = 131.88 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-01-17
Diffraction Radiation
Monochromator Protocol
Numerical link type Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 PHOTON FACTORY BL-5A

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
1.8 75.8 98.3 -- -- -- -- 104764 102983 0.0 0.0 --
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)
1.8 1.9 97.4 -- -- -- -- --

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 1.8 65.82 -- 0.0 99532 97850 5130 98.31 -- 0.16532 0.16398 0.19052 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 1.8 1.847 -- 365 7100 0.229 0.277 -- 97.01
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.7
Anisotropic B[1][1] -0.86
Anisotropic B[1][2] -0.86
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.79
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.01
r_chiral_restr 0.134
r_dihedral_angle_4_deg 25.912
r_dihedral_angle_3_deg 13.801
r_dihedral_angle_2_deg 37.195
r_dihedral_angle_1_deg 5.382
r_angle_other_deg 0.983
r_angle_refined_deg 1.719
r_bond_other_d 0.005
r_bond_refined_d 0.022
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6986
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 934

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
Molrep model building
ADSC version: Quantum data collection