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_plane_restr 0.007
f_chiral_restr 0.076
f_angle_d 1.357
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

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1026) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction