X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.15
Details 27.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.75, 5% glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.21 α = 90
b = 77.56 β = 97.77
c = 94.94 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-09-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA

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
2.77 48.75 99.2 0.071 -- -- 5.1 -- 27487 -- -- 82.0
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)
2.77 2.92 99.3 0.758 -- 2.0 5.1 --

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 2.77 48.75 -- -- -- 26116 1357 99.05 -- 0.21993 0.21776 0.2616 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 2.77 2.842 -- 101 1900 0.327 0.362 -- 99.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 108.746
Anisotropic B[1][1] 3.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.81
Anisotropic B[2][2] 0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.28
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.033
r_bond_refined_d 0.009
r_scbond_other 3.081
r_gen_planes_other 0.004
r_long_range_B_refined 7.189
r_mcbond_it 2.987
r_chiral_restr 0.038
r_scbond_it 3.081
r_dihedral_angle_1_deg 7.812
r_mcangle_it 4.761
r_dihedral_angle_4_deg 19.171
r_gen_planes_refined 0.01
r_angle_refined_deg 1.098
r_dihedral_angle_3_deg 15.867
r_long_range_B_other 7.189
r_dihedral_angle_2_deg 29.954
r_mcangle_other 4.761
r_scangle_other 4.997
r_bond_other_d 0.001
r_mcbond_other 2.987
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8141
Nucleic Acid Atoms 0
Heterogen Atoms 148
Solvent Atoms 18

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0232
XDS data reduction
Aimless data scaling
PHASER phasing