X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 294.0
Details 0.12 M Monosaccharides, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.86 α = 90
b = 81.33 β = 90
c = 168.59 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2018-01-19
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
2.49 81.34 100.0 0.077 -- -- 13.0 -- 39789 -- -- --
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)
2.49 2.55 100.0 0.948 -- 2.3 12.8 --

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 2.49 81.34 -- -- -- 37771 1953 99.94 -- 0.22013 0.21796 0.26258 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 2.49 2.554 -- 173 2710 0.39 0.368 -- 99.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 82.556
Anisotropic B[1][1] 4.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.78
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 15.842
r_gen_planes_other 0.001
r_scbond_other 2.312
r_dihedral_angle_2_deg 30.09
r_mcangle_it 4.819
r_bond_refined_d 0.007
r_scangle_other 3.979
r_angle_refined_deg 1.138
r_mcbond_it 2.839
r_angle_other_deg 0.89
r_scbond_it 2.313
r_long_range_B_other 6.976
r_chiral_restr 0.06
r_gen_planes_refined 0.005
r_mcbond_other 2.84
r_mcangle_other 4.819
r_long_range_B_refined 6.976
r_dihedral_angle_1_deg 5.861
r_bond_other_d 0.001
r_dihedral_angle_3_deg 13.408
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7531
Nucleic Acid Atoms 0
Heterogen Atoms 114
Solvent Atoms 106

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
DIALS data reduction
Aimless data scaling
PHASER phasing