X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 1.5M ammonium phosphate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.1 α = 90
b = 58.34 β = 109.65
c = 137.91 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPRING-8 BL44XU

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
1.75 50 98.7 0.073 -- -- 3.8 -- 121695 -- -- --
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)
1.75 1.81 87.5 0.434 -- -- 3.2 10747

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 1.75 44.69 -- 0.0 -- 121183 6097 98.19 -- 0.1621 0.1596 0.2087 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 1.751 1.796 -- 356 6713 0.242 0.277 -- 79.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.6904
Anisotropic B[1][1] 0.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.13
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.014
r_chiral_restr 0.179
r_dihedral_angle_4_deg 17.011
r_dihedral_angle_3_deg 14.245
r_dihedral_angle_2_deg 36.073
r_dihedral_angle_1_deg 6.965
r_angle_refined_deg 2.276
r_bond_refined_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9207
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 1082

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.6.0117 refinement
HKL data reduction