X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 277.0
Details well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.84 α = 90
b = 89.84 β = 90
c = 106.61 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2016-09-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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
1.94 77.81 100.0 0.127 -- -- -- -- 71098 -- -3.0 32.19
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)
1.94 2.06 99.8 1.095 -- 1.28 -- --

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 1.941 62.848 -- 1.37 -- 37251 1469 99.95 -- 0.1983 0.197 0.2301 --
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 1.9415 2.0109 -- 146 3517 0.2557 0.2829 -- 100.0
X Ray Diffraction 2.0109 2.0914 -- 145 3541 0.2376 0.2453 -- 100.0
X Ray Diffraction 2.0914 2.1866 -- 145 3538 0.2452 0.2999 -- 100.0
X Ray Diffraction 2.1866 2.3019 -- 144 3527 0.2268 0.321 -- 100.0
X Ray Diffraction 2.3019 2.4461 -- 148 3555 0.2198 0.2671 -- 100.0
X Ray Diffraction 2.4461 2.635 -- 150 3559 0.1998 0.2151 -- 100.0
X Ray Diffraction 2.635 2.9001 -- 146 3581 0.1909 0.249 -- 100.0
X Ray Diffraction 2.9001 3.3198 -- 146 3584 0.1904 0.2072 -- 100.0
X Ray Diffraction 3.3198 4.1825 -- 146 3602 0.1744 0.2134 -- 100.0
X Ray Diffraction 4.1825 62.8808 -- 153 3778 0.1882 0.2061 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.9238
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.106
f_plane_restr 0.008
f_dihedral_angle_d 20.035
f_bond_d 0.017
f_angle_d 1.612
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2317
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 220

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
XSCALE data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.22
XDS data reduction