X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9.5
Temperature 293.0
Details 30mg/ml protein, 0.1M Tris HCl, 0.1M Lithium sulfate, 30% PEG6000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.7 α = 97.7
b = 48.6 β = 100.4
c = 65.2 γ = 106.3
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Platinum-coated silicon bent mirrors 2002-10-05
Diffraction Radiation
Monochromator Protocol
Rotated-inclined focusing S(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.0 PHOTON FACTORY BL-6B

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
1.5 55.9 92.1 0.062 -- -- -- -- 76333 -- -- 24.07

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 1.5 20.0 -- -- -- 66166 3515 94.02 -- 0.20386 0.20222 0.23493 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 1.5 1.539 4054 222 4054 0.319 0.315 -- 78.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.812
Anisotropic B[1][1] 1.18
Anisotropic B[1][2] 0.63
Anisotropic B[1][3] -0.64
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] -0.97
Anisotropic B[3][3] -0.94
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_chiral_restr 0.093
r_dihedral_angle_4_deg 19.828
r_dihedral_angle_3_deg 12.819
r_dihedral_angle_2_deg 32.398
r_dihedral_angle_1_deg 5.537
r_angle_refined_deg 1.336
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3678
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 592

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
PROCESS Data Reduction (intensity integration)
PROCESS 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
CrystalClear data collection