X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 290.0
Details 49%-51% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MnSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.83 α = 90
b = 109.33 β = 90
c = 150.11 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-03-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.1158 ALS 12.3.1

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
1.57 100 92.9 0.048 -- -- 8.6 -- 199455 -- -3.0 27.766
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)
1.57 1.66 99.9 0.462 -- 3.75 -- --

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
FOURIER SYNTHESIS 1.57 79.565 -- 2.35 -- 191796 8791 89.3 -- 0.1803 0.1792 0.2036 Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 resolution
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 1.57 1.5878 -- 305 5800 0.258 0.2784 -- 86.0
X Ray Diffraction 1.5878 1.6065 -- 315 5984 0.2379 0.2388 -- 89.0
X Ray Diffraction 1.6065 1.6261 -- 316 5999 0.2265 0.2589 -- 89.0
X Ray Diffraction 1.6261 1.6467 -- 324 6161 0.2223 0.2392 -- 91.0
X Ray Diffraction 1.6467 1.6684 -- 325 6178 0.2171 0.249 -- 92.0
X Ray Diffraction 1.6684 1.6912 -- 329 6254 0.2107 0.2424 -- 93.0
X Ray Diffraction 1.6912 1.7154 -- 333 6324 0.2112 0.2454 -- 94.0
X Ray Diffraction 1.7154 1.741 -- 335 6358 0.2069 0.2446 -- 94.0
X Ray Diffraction 1.741 1.7682 -- 338 6423 0.2009 0.2199 -- 95.0
X Ray Diffraction 1.7682 1.7972 -- 337 6417 0.1891 0.2142 -- 95.0
X Ray Diffraction 1.7972 1.8282 -- 342 6482 0.1874 0.2263 -- 96.0
X Ray Diffraction 1.8282 1.8614 -- 340 6464 0.187 0.2248 -- 96.0
X Ray Diffraction 1.8614 1.8972 -- 273 5187 0.1859 0.2171 -- 83.0
X Ray Diffraction 1.936 1.9781 -- 263 5010 0.1834 0.2319 -- 91.0
X Ray Diffraction 1.9781 2.0241 -- 256 6767 0.1779 0.213 -- 98.0
X Ray Diffraction 2.0241 2.0747 -- 239 6775 0.1691 0.175 -- 99.0
X Ray Diffraction 2.0747 2.1308 -- 271 6835 0.1688 0.1882 -- 99.0
X Ray Diffraction 2.1308 2.1935 -- 271 6775 0.1688 0.1962 -- 99.0
X Ray Diffraction 2.1935 2.2643 -- 151 2901 0.1673 0.191 -- 88.0
X Ray Diffraction 2.2643 2.3453 -- 215 5705 0.1677 0.2016 -- 96.0
X Ray Diffraction 2.3453 2.4392 -- 273 6826 0.1692 0.1926 -- 99.0
X Ray Diffraction 2.4392 2.5502 -- 280 6834 0.1681 0.1848 -- 99.0
X Ray Diffraction 2.5502 2.6846 -- 286 6898 0.1766 0.2053 -- 100.0
X Ray Diffraction 2.6846 2.8528 -- 307 6862 0.1851 0.2195 -- 100.0
X Ray Diffraction 2.8528 3.0731 -- 331 6844 0.1858 0.2198 -- 100.0
X Ray Diffraction 3.0731 3.3824 -- 356 6871 0.1745 0.1977 -- 100.0
X Ray Diffraction 3.3824 3.8718 -- 345 6918 0.164 0.1866 -- 100.0
X Ray Diffraction 3.8718 4.878 -- 365 6950 0.1513 0.1806 -- 100.0
X Ray Diffraction 4.878 79.6673 -- 370 7203 0.2005 0.1987 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.236
f_chiral_restr 0.076
f_angle_d 1.357
f_plane_restr 0.007
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9185
Nucleic Acid Atoms 850
Heterogen Atoms 58
Solvent Atoms 1365

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_1026
PDB_EXTRACT data extraction version: 3.11
XDS data reduction