X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 291.0
Details 2.2-2.4 M sodium/potassium phosphate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.1 α = 90
b = 72.1 β = 90
c = 99.2 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M -- 2016-12-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24

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
1.9 45.34 99.3 0.045 -- -- 3.8 -- 21069 -- -- --
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)
1.9 1.94 -- -- -- -- -- --

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 1.9 45.34 -- -- -- 19952 1084 98.91 -- 0.1916 0.18952 0.23101 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 1.9 1.949 -- 91 1431 0.262 0.283 -- 98.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.775
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.64
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.109
r_bond_refined_d 0.015
r_dihedral_angle_3_deg 14.74
r_mcangle_it 2.229
r_mcbond_other 1.402
r_angle_refined_deg 1.898
r_angle_other_deg 1.314
r_dihedral_angle_1_deg 6.165
r_gen_planes_refined 0.007
r_bond_other_d 0.004
r_long_range_B_refined 6.237
r_long_range_B_other 6.238
r_scbond_other 2.248
r_dihedral_angle_2_deg 26.914
r_scbond_it 2.248
r_dihedral_angle_4_deg 16.328
r_mcangle_other 2.228
r_gen_planes_other 0.002
r_mcbond_it 1.402
r_scangle_other 3.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1615
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 161

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XDS data reduction
Aimless data scaling
REFMAC phasing