X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 18% PEG4000 20% 2-propanol 0.1 M Na-citrate pH 5.6 Protein sample buffer: 20 mM HEPES, 150 mM NaCl, pH 7.4 supplemented with 10 mM CoASH

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.5 α = 90
b = 127.03 β = 90
c = 143.8 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 PILATUS3 2M -- 2017-10-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA

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
2.91 47.93 99.5 -- -- -- 6.5 -- 48328 -- -- 84.77
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)
2.91 3.08 97.8 -- -- 0.83 -- --

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 2.91 47.6 -- 0.0 -- 48218 2409 99.9 -- 0.191 0.189 0.223 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 2.91 2.99 -- 175 3304 0.24 0.265 0.0 99.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 99.16
Anisotropic B[1][1] 21.1312
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.4913
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -22.6225
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_angle_deg 1.21
t_omega_torsion 2.88
t_other_torsion 19.51
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11552
Nucleic Acid Atoms 0
Heterogen Atoms 149
Solvent Atoms 0

Software

Software
Software Name Purpose
BUSTER refinement version: 2.10.2
XDS data reduction
Aimless data scaling
PHASER phasing