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 = 49.13 α = 79.86
b = 59.63 β = 81.64
c = 79.62 γ = 76.07
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 -- 2018-07-29
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
1.5 47.41 88.0 0.031 -- -- 1.7 -- 119825 -- -- --
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)
1.5 1.59 93.8 1.358 -- -- 1.4 18692

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 1.5 77.92 -- 0.0 -- 113734 6091 87.94 -- 0.2242 0.2226 0.2554 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 1.505 1.544 -- 486 8883 0.415 0.443 -- 93.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.675
Anisotropic B[1][1] 2.7
Anisotropic B[1][2] 0.87
Anisotropic B[1][3] -0.29
Anisotropic B[2][2] -0.82
Anisotropic B[2][3] 0.88
Anisotropic B[3][3] -1.09
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_bond_other_d 0.002
r_angle_refined_deg 1.867
r_chiral_restr 0.111
r_mcbond_it 2.996
r_dihedral_angle_4_deg 12.338
r_gen_planes_refined 0.009
r_mcangle_it 4.069
r_dihedral_angle_3_deg 15.119
r_gen_planes_other 0.002
r_dihedral_angle_1_deg 6.88
r_mcbond_other 2.996
r_angle_other_deg 1.008
r_dihedral_angle_2_deg 38.147
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5758
Nucleic Acid Atoms 0
Heterogen Atoms 69
Solvent Atoms 262

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