X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 291.0
Details 2microlitres of 15mg/ml protein in 20mM Tris buffer, pH8, with an equivalent volume of reservoir solution containing 0.1M Tris, 2.4M Ammonium sulfate pH8

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.62 α = 90
b = 81.65 β = 90
c = 85.26 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-F -- 2017-03-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928 Diamond I04-1

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
1.36 46.62 99.9 0.043 -- -- 5.4 -- 70585 -- -- 16.0
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)
1.36 1.38 98.5 1.048 -- 1.2 4.4 --

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
SAD 1.36 42.67 -- 0.0 -- 68885 1103 99.03 -- 0.1969 0.1965 0.2237 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 1.36 1.395 -- 91 4910 0.397 0.385 -- 96.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.701
Anisotropic B[1][1] 0.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.12
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.021
r_bond_other_d 0.001
r_angle_refined_deg 1.84
r_dihedral_angle_3_deg 13.404
r_mcbond_other 1.677
r_dihedral_angle_2_deg 28.652
r_angle_other_deg 1.557
r_mcangle_it 2.401
r_dihedral_angle_1_deg 17.623
r_gen_planes_other 0.066
r_gen_planes_refined 0.024
r_dihedral_angle_4_deg 14.139
r_chiral_restr 0.084
r_mcbond_it 1.699
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2159
Nucleic Acid Atoms 0
Heterogen Atoms 97
Solvent Atoms 250

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0230
PDB_EXTRACT data extraction version: 3.22
xia2 data reduction
Aimless data scaling
Auto-Rickshaw phasing