X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 50mM sodium citrate (pH 4.6), 2.0M ammonium sulfate supplemented with 5% PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.85 α = 90
b = 120.85 β = 90
c = 42.63 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2013-04-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1

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
1.13 50 97.8 0.083 -- -- 3.6 -- 73602 -- -- --
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)
1.13 -- -- 0.45 -- -- -- --

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 1.18 50.0 -- -- -- 69904 3695 95.9 -- 0.198 0.197 0.228 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 1.18 1.21 -- 157 3036 0.289 0.32 -- 56.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.26
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] -0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.33
RMS Deviations
Key Refinement Restraint Deviation
r_rigid_bond_restr 5.765
r_dihedral_angle_2_deg 34.037
r_bond_other_d 0.003
r_mcbond_it 0.887
r_scangle_other 1.199
r_sphericity_bonded 4.575
r_angle_other_deg 0.929
r_scbond_it 1.114
r_long_range_B_other 2.074
r_scbond_other 1.111
r_long_range_B_refined 2.075
r_mcbond_other 0.884
r_chiral_restr 0.077
r_dihedral_angle_1_deg 6.596
r_dihedral_angle_3_deg 14.108
r_gen_planes_other 0.002
r_dihedral_angle_4_deg 16.0
r_mcangle_it 1.094
r_sphericity_free 17.309
r_gen_planes_refined 0.006
r_angle_refined_deg 1.405
r_bond_refined_d 0.008
r_mcangle_other 1.094
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1942
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 214

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0103
HKL-2000 data processing