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 = 106.55 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
1.51 62.81 99.9 0.06 -- -- -- -- 149826 -- -3.0 24.25
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)
1.51 1.6 99.6 1.097 -- 1.13 -- --

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 1.513 44.89 -- 1.36 -- 77783 3060 99.94 -- 0.1906 0.1897 0.2132 --
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 1.5127 1.5363 -- 142 3298 0.3247 0.3386 -- 100.0
X Ray Diffraction 1.5363 1.5615 -- 133 3354 0.302 0.3213 -- 100.0
X Ray Diffraction 1.5615 1.5884 -- 137 3388 0.2826 0.2981 -- 100.0
X Ray Diffraction 1.5884 1.6173 -- 143 3357 0.2688 0.2716 -- 100.0
X Ray Diffraction 1.6173 1.6484 -- 131 3360 0.2435 0.2779 -- 100.0
X Ray Diffraction 1.6484 1.6821 -- 132 3363 0.2537 0.2515 -- 100.0
X Ray Diffraction 1.6821 1.7186 -- 142 3377 0.2478 0.2687 -- 100.0
X Ray Diffraction 1.7186 1.7586 -- 142 3375 0.2438 0.2965 -- 100.0
X Ray Diffraction 1.7586 1.8026 -- 136 3365 0.2234 0.2621 -- 100.0
X Ray Diffraction 1.8026 1.8513 -- 135 3364 0.2079 0.2106 -- 100.0
X Ray Diffraction 1.8513 1.9058 -- 139 3396 0.1962 0.2328 -- 100.0
X Ray Diffraction 1.9058 1.9673 -- 137 3374 0.1907 0.2309 -- 100.0
X Ray Diffraction 1.9673 2.0376 -- 141 3375 0.2033 0.2444 -- 100.0
X Ray Diffraction 2.0376 2.1192 -- 140 3393 0.196 0.2432 -- 100.0
X Ray Diffraction 2.1192 2.2157 -- 139 3394 0.1907 0.2227 -- 100.0
X Ray Diffraction 2.2157 2.3325 -- 139 3395 0.1831 0.1922 -- 100.0
X Ray Diffraction 2.3325 2.4786 -- 142 3419 0.1763 0.2031 -- 100.0
X Ray Diffraction 2.4786 2.67 -- 141 3400 0.1733 0.175 -- 100.0
X Ray Diffraction 2.67 2.9386 -- 143 3436 0.1773 0.1999 -- 100.0
X Ray Diffraction 2.9386 3.3637 -- 138 3436 0.174 0.1651 -- 100.0
X Ray Diffraction 3.3637 4.2374 -- 142 3491 0.167 0.2047 -- 100.0
X Ray Diffraction 4.2374 44.9103 -- 146 3613 0.1897 0.2179 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.8431
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.314
f_dihedral_angle_d 17.589
f_bond_d 0.018
f_angle_d 1.692
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2323
Nucleic Acid Atoms 0
Heterogen Atoms 148
Solvent Atoms 329

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