X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.34 α = 90
b = 90.34 β = 90
c = 216 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 PILATUS 6M-F -- 2018-02-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04

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
2.07 78.36 100.0 0.124 -- -- 12.2 -- 63220 -- -- --
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)
2.07 2.12 -- -- -- 1.0 -- --

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 2.07 78.36 -- -- -- 60057 3072 99.94 -- 0.18298 0.18007 0.2416 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 2.07 2.124 -- 225 4347 0.341 0.352 -- 99.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.243
Anisotropic B[1][1] 1.64
Anisotropic B[1][2] 0.82
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.31
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.568
r_gen_planes_refined 0.007
r_chiral_restr 0.074
r_bond_other_d 0.002
r_mcangle_it 5.105
r_dihedral_angle_1_deg 7.501
r_dihedral_angle_2_deg 35.049
r_gen_planes_other 0.002
r_bond_refined_d 0.008
r_mcbond_it 3.897
r_mcangle_other 5.105
r_scbond_it 4.86
r_dihedral_angle_4_deg 16.481
r_mcbond_other 3.893
r_long_range_B_refined 7.909
r_long_range_B_other 7.908
r_scbond_other 4.859
r_dihedral_angle_3_deg 14.98
r_scangle_other 6.646
r_angle_other_deg 1.296
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6242
Nucleic Acid Atoms 0
Heterogen Atoms 409
Solvent Atoms 272

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
xia2 data reduction
Aimless data scaling
MOLREP phasing