X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 289.0
Details 22% polyethylene glycol monomethylether 5000, 80 mM Bis-Tris pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.26 α = 90
b = 62.26 β = 90
c = 73.58 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M -- 2019-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24

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
1.81 43.5 100.0 0.09 -- -- 10.3 -- 15507 -- -- --
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)
1.81 1.86 98.4 2.045 -- 1.1 5.8 --

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 1.81 43.49 -- 0.0 -- 14703 763 99.7 -- 0.1967 0.1942 0.2441 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 1.81 1.856 -- 39 1062 0.304 0.354 0.0 97.43
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.437
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.85
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 3.839
r_gen_planes_refined 0.011
r_angle_other_deg 1.405
r_bond_refined_d 0.013
r_angle_refined_deg 1.873
r_dihedral_angle_2_deg 37.395
r_chiral_restr 0.096
r_dihedral_angle_3_deg 17.09
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.989
r_bond_other_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1249
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 44

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
PDB_EXTRACT data extraction version: 3.22
DIALS data reduction
Aimless data scaling
PHASER phasing