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 = 89.78 α = 90
b = 89.78 β = 90
c = 106.34 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
1.65 77.75 99.9 0.054 -- -- -- -- 114368 -- -3.0 29.19
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)
1.65 1.75 99.5 0.94 -- 1.05 -- --

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 1.654 44.888 -- 1.37 -- 59554 2342 99.94 -- 0.1882 0.1872 0.2125 --
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 1.6542 1.688 -- 136 3282 0.308 0.3075 -- 99.0
X Ray Diffraction 1.688 1.7247 -- 139 3344 0.2768 0.2878 -- 100.0
X Ray Diffraction 1.7247 1.7648 -- 131 3323 0.2833 0.3285 -- 100.0
X Ray Diffraction 1.7648 1.8089 -- 141 3329 0.2674 0.2875 -- 100.0
X Ray Diffraction 1.8089 1.8578 -- 130 3344 0.2388 0.264 -- 100.0
X Ray Diffraction 1.8578 1.9125 -- 139 3338 0.2151 0.2345 -- 100.0
X Ray Diffraction 1.9125 1.9742 -- 133 3302 0.193 0.2323 -- 100.0
X Ray Diffraction 1.9742 2.0448 -- 143 3386 0.2039 0.2433 -- 100.0
X Ray Diffraction 2.0448 2.1267 -- 133 3330 0.1956 0.2315 -- 100.0
X Ray Diffraction 2.1267 2.2235 -- 141 3343 0.1873 0.2157 -- 100.0
X Ray Diffraction 2.2235 2.3407 -- 138 3334 0.1821 0.2047 -- 100.0
X Ray Diffraction 2.3407 2.4873 -- 136 3403 0.1776 0.2167 -- 100.0
X Ray Diffraction 2.4873 2.6793 -- 145 3354 0.1721 0.1647 -- 100.0
X Ray Diffraction 2.6793 2.9489 -- 139 3383 0.1789 0.212 -- 100.0
X Ray Diffraction 2.9489 3.3755 -- 136 3402 0.1774 0.1885 -- 100.0
X Ray Diffraction 3.3755 4.2523 -- 140 3453 0.1646 0.1963 -- 100.0
X Ray Diffraction 4.2523 44.904 -- 142 3562 0.1908 0.2196 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.4399
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.652
f_bond_d 0.019
f_angle_d 1.933
f_plane_restr 0.011
f_chiral_restr 0.143
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2385
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 280

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