X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 24-24.5% PEG 3350, 160 mM MgCl2, 0.1 M Bis Tris pH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.57 α = 90
b = 84.57 β = 90
c = 117.66 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M mirrors 2017-09-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97858 SOLEIL PROXIMA 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
2 45.87 99.3 0.062 -- -- 2.9 -- 63507 -- -- --
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)
2.0 2.05 95.1 0.824 -- -- 2.8 --

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 2.2 45.87 -- -- -- 45421 2320 99.9 -- 0.17659 0.17435 0.22076 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 2.2 2.257 -- 146 3398 0.261 0.321 -- 99.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.082
Anisotropic B[1][1] 0.93
Anisotropic B[1][2] 0.46
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.01
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.005
r_angle_refined_deg 1.495
r_dihedral_angle_4_deg 16.937
r_long_range_B_other 7.017
r_scbond_other 3.674
r_scangle_other 5.479
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 14.169
r_bond_other_d 0.002
r_angle_other_deg 2.034
r_mcangle_other 4.477
r_dihedral_angle_1_deg 5.898
r_mcbond_it 3.249
r_dihedral_angle_2_deg 36.306
r_long_range_B_refined 7.011
r_chiral_restr 0.092
r_scbond_it 3.675
r_gen_planes_refined 0.007
r_mcangle_it 4.478
r_mcbond_other 3.249
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7953
Nucleic Acid Atoms 0
Heterogen Atoms 105
Solvent Atoms 453

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
XDS data reduction
Aimless data scaling version: 0.5.32
PHASER phasing
PDB_EXTRACT data extraction version: 3.24