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_bond_refined_d 0.011
r_dihedral_angle_4_deg 19.828
r_angle_refined_deg 1.336
r_chiral_restr 0.093
r_gen_planes_refined 0.008
r_dihedral_angle_1_deg 5.537
r_dihedral_angle_3_deg 12.819
r_dihedral_angle_2_deg 32.398
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

Software
Software Name Purpose
CrystalClear data collection
MOLREP phasing
REFMAC refinement version: 5.7.0029
PROCESS data reduction
PROCESS data scaling