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 = 89.69 α = 90
b = 89.69 β = 90
c = 106.4 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
1.79 77.68 100.0 0.082 -- -- -- -- 90558 -- -3.0 32.41
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)
1.79 1.9 99.9 1.038 -- 1.07 -- --

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 1.788 44.846 -- 1.37 -- 47295 1860 99.98 -- 0.1919 0.1907 0.2236 --
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 1.7881 1.8364 -- 136 3467 0.3351 0.3364 -- 100.0
X Ray Diffraction 1.8364 1.8905 -- 142 3437 0.2908 0.3037 -- 100.0
X Ray Diffraction 1.8905 1.9515 -- 140 3467 0.2562 0.2496 -- 100.0
X Ray Diffraction 1.9515 2.0212 -- 145 3445 0.2368 0.2722 -- 100.0
X Ray Diffraction 2.0212 2.1021 -- 143 3462 0.2216 0.2614 -- 100.0
X Ray Diffraction 2.1021 2.1978 -- 141 3475 0.2115 0.2803 -- 100.0
X Ray Diffraction 2.1978 2.3137 -- 144 3470 0.1897 0.2168 -- 100.0
X Ray Diffraction 2.3137 2.4586 -- 142 3440 0.1859 0.2408 -- 100.0
X Ray Diffraction 2.4586 2.6485 -- 148 3506 0.1814 0.1891 -- 100.0
X Ray Diffraction 2.6485 2.9149 -- 142 3486 0.1822 0.2179 -- 100.0
X Ray Diffraction 2.9149 3.3366 -- 144 3535 0.1823 0.1943 -- 100.0
X Ray Diffraction 3.3366 4.2033 -- 142 3562 0.1702 0.2199 -- 100.0
X Ray Diffraction 4.2033 44.8601 -- 151 3683 0.1832 0.2147 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.7235
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.018
f_dihedral_angle_d 19.009
f_angle_d 1.886
f_plane_restr 0.011
f_chiral_restr 0.144
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2317
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 254

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