X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 295.0
Details 0.085 M HEPES sodium salt (pH 7.5), 8.5% (v/v) isopropanol, 17% (w/v) PEG 4000 and 15% (v/v) glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.3 α = 90
b = 121.3 β = 90
c = 53.4 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2015-04-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
2.9 47.6 100.0 0.12 -- -- 5.8 -- 6484 -- -- 49.33
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)
2.9 3.08 100.0 0.526 -- 3.7 5.8 1026

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 2.9 47.603 -- 2.0 -- 6482 367 99.97 -- 0.1907 0.1882 0.2318 --
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 2.9002 3.3198 -- 124 2024 0.2305 0.2966 -- 100.0
X Ray Diffraction 3.3198 4.1822 -- 114 2060 0.1895 0.2328 -- 100.0
X Ray Diffraction 4.1822 47.609 -- 129 2031 0.1707 0.2064 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.012
f_angle_d 1.27
f_dihedral_angle_d 15.444
f_chiral_restr 0.055
f_plane_restr 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1822
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 13

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
Aimless data scaling version: 0.5.8
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
PHASER phasing