X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.26 α = 90
b = 131.38 β = 90
c = 159.87 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 2M -- 2018-03-08
Diffraction Radiation
Monochromator Protocol
KMC-2 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2

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
1.81 50 98.8 0.073 -- -- 6.7 -- 96547 -3.0 -3.0 --
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)
1.81 1.92 93.4 0.849 -- 1.94 6.0 --

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
FOURIER SYNTHESIS 1.81 47.26 -- -- -- 94359 2099 98.67 -- 0.15045 0.14983 0.17756 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 1.811 1.858 -- 133 6021 0.369 0.324 -- 85.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.915
Anisotropic B[1][1] 1.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.43
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 1.824
r_dihedral_angle_3_deg 14.757
r_angle_refined_deg 1.802
r_dihedral_angle_4_deg 16.041
r_chiral_restr 0.112
r_long_range_B_other 5.442
r_gen_planes_other 0.002
r_long_range_B_refined 5.442
r_scangle_other 3.806
r_dihedral_angle_2_deg 36.077
r_mcangle_it 2.548
r_bond_refined_d 0.017
r_dihedral_angle_1_deg 6.663
r_mcbond_it 1.824
r_mcangle_other 2.548
r_bond_other_d 0.003
r_angle_other_deg 1.357
r_scbond_it 2.507
r_scbond_other 2.507
r_gen_planes_refined 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5546
Nucleic Acid Atoms 0
Heterogen Atoms 321
Solvent Atoms 427

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction
XDS data scaling
REFMAC phasing
Coot model building