X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 5% (v/v) ethonal, 28% PEG20000 100 mM MES pH7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.86 α = 90
b = 95.46 β = 90
c = 72.38 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2018-11-17
Diffraction Radiation
Monochromator Protocol
-- 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
1.9 47.73 99.8 0.067 -- -- 6.3 -- 18576 -- -- --
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)
1.9 1.94 97.4 0.46 -- 3.5 5.0 --

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 1.9 47.73 -- -- -- 17640 916 99.8 -- 0.15852 0.15667 0.19352 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 1.901 1.95 -- 65 1263 0.22 0.282 -- 97.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.962
Anisotropic B[1][1] -1.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.1
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.305
r_scbond_other 3.09
r_dihedral_angle_2_deg 36.427
r_gen_planes_other 0.002
r_bond_other_d 0.002
r_long_range_B_other 5.649
r_mcbond_other 2.087
r_dihedral_angle_3_deg 12.482
r_angle_other_deg 0.965
r_scangle_other 4.254
r_angle_refined_deg 1.872
r_mcangle_other 2.851
r_mcangle_it 2.851
r_bond_refined_d 0.018
r_gen_planes_refined 0.008
r_long_range_B_refined 6.142
r_dihedral_angle_4_deg 19.085
r_mcbond_it 2.098
r_chiral_restr 0.241
r_dihedral_angle_1_deg 7.469
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1854
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 256

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction
XDS data scaling
PHENIX phasing