X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 290.0
Details Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.75 α = 89.9
b = 83.31 β = 89.05
c = 86.75 γ = 88.7
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 -- 2018-07-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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
2.8 19.76 95.74 0.03857 -- -- 1.8 -- 32828 -- -- --
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)
2.8 2.9 -- 0.3994 -- -- -- --

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 2.8 19.76 -- -- -- 32828 2003 95.74 -- -- 0.2092 0.2495 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 2.8 2.9 -- 197 3279 0.3203 0.3655 -- 96.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.03
Anisotropic B[1][1] 2.1
Anisotropic B[1][2] 1.96
Anisotropic B[1][3] -0.31
Anisotropic B[2][2] -0.84
Anisotropic B[2][3] 2.67
Anisotropic B[3][3] -1.18
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.827
r_dihedral_angle_1_deg 5.538
r_scbond_other 5.568
r_dihedral_angle_3_deg 13.489
r_mcbond_other 5.226
r_chiral_restr 0.054
r_mcbond_it 5.228
r_angle_refined_deg 1.259
r_scbond_it 5.569
r_dihedral_angle_2_deg 26.251
r_dihedral_angle_4_deg 14.605
r_mcangle_it 7.985
r_gen_planes_other 0.002
r_bond_other_d 0.002
r_long_range_B_refined 11.413
r_scangle_other 8.56
r_gen_planes_refined 0.007
r_bond_refined_d 0.007
r_long_range_B_other 11.412
r_mcangle_other 7.985
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9443
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 6

Software

Software
Software Name Purpose
PHENIX refinement
XDS data reduction
XDS data scaling
PHASER phasing