X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.15
Details 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.89 α = 79.68
b = 59.51 β = 82.07
c = 79.98 γ = 76.2
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-07-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1

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
1.66 49.9 96.6 0.041 -- -- 1.8 -- 97841 -- -- --
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)
1.66 1.7 95.1 0.69 -- -- 1.7 7176

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
FOURIER SYNTHESIS 1.66 78.29 -- 0.0 -- 92891 4950 96.53 -- 0.2093 0.2076 0.2408 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 1.66 1.703 -- 402 6763 0.348 0.346 -- 95.04
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.505
Anisotropic B[1][1] 2.54
Anisotropic B[1][2] 0.72
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] -0.6
Anisotropic B[2][3] 1.07
Anisotropic B[3][3] -1.1
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.054
r_bond_other_d 0.002
r_chiral_restr 0.12
r_gen_planes_refined 0.01
r_dihedral_angle_3_deg 15.069
r_bond_refined_d 0.018
r_dihedral_angle_2_deg 36.684
r_mcbond_it 2.794
r_gen_planes_other 0.002
r_angle_refined_deg 1.958
r_dihedral_angle_1_deg 7.022
r_mcangle_it 3.927
r_mcbond_other 2.817
r_dihedral_angle_4_deg 14.077
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5786
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 289

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
Aimless data scaling version: 0.7.1
PDB_EXTRACT data extraction version: 3.23
XDS data reduction
REFMAC phasing