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 48%-54% Saturated Ammonium Sulfate, 2.5% MPD, 10mM MgSO4, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.67 α = 90
b = 109.37 β = 90
c = 150.39 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-11-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM

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
1.64 50 91.2 0.038 -- -- 5.7 -- 172238 -- -3.0 29.803
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)
1.64 1.74 99.9 0.476 -- 3.98 -- --

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 1.64 30.982 -- 2.35 -- 165495 7474 87.69 -- 0.1821 0.1811 0.2034 Inherited free reflections from 2HVI plus 5% randomly generated reflections beyond 1.98 A 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 1.64 1.6586 -- 268 5102 0.2411 0.2607 -- 86.0
X Ray Diffraction 1.6586 1.6782 -- 273 5187 0.2307 0.2662 -- 88.0
X Ray Diffraction 1.6782 1.6986 -- 276 5235 0.2224 0.2423 -- 89.0
X Ray Diffraction 1.6986 1.7201 -- 283 5382 0.2116 0.2403 -- 90.0
X Ray Diffraction 1.7201 1.7427 -- 282 5357 0.2047 0.2515 -- 91.0
X Ray Diffraction 1.7427 1.7666 -- 291 5538 0.2041 0.2448 -- 93.0
X Ray Diffraction 1.7666 1.7919 -- 291 5529 0.1989 0.2463 -- 94.0
X Ray Diffraction 1.7919 1.8186 -- 294 5570 0.1933 0.2194 -- 94.0
X Ray Diffraction 1.8186 1.847 -- 294 5601 0.1993 0.2505 -- 94.0
X Ray Diffraction 1.847 1.8773 -- 293 5556 0.1929 0.2467 -- 94.0
X Ray Diffraction 1.8773 1.9097 -- 98 1860 0.1971 0.2323 -- 85.0
X Ray Diffraction 1.9444 1.9818 -- 285 5396 0.1946 0.2384 -- 91.0
X Ray Diffraction 1.9818 2.0222 -- 186 5921 0.1859 0.2069 -- 98.0
X Ray Diffraction 2.0222 2.0662 -- 210 5966 0.1834 0.214 -- 99.0
X Ray Diffraction 2.0662 2.1142 -- 235 5934 0.1761 0.1879 -- 99.0
X Ray Diffraction 2.1142 2.1671 -- 241 5969 0.1737 0.191 -- 99.0
X Ray Diffraction 2.1671 2.2257 -- 251 5292 0.1768 0.2069 -- 96.0
X Ray Diffraction 2.2257 2.2911 -- 38 1190 0.1667 0.1844 -- 86.0
X Ray Diffraction 2.2911 2.3651 -- 234 5966 0.171 0.1985 -- 99.0
X Ray Diffraction 2.3651 2.4496 -- 241 6007 0.1733 0.1958 -- 99.0
X Ray Diffraction 2.4496 2.5476 -- 249 5995 0.1741 0.202 -- 99.0
X Ray Diffraction 2.5476 2.6635 -- 255 6035 0.1786 0.1907 -- 99.0
X Ray Diffraction 2.6635 2.8038 -- 259 6009 0.1913 0.2045 -- 99.0
X Ray Diffraction 2.8038 2.9794 -- 282 6010 0.1926 0.2282 -- 100.0
X Ray Diffraction 2.9794 3.2092 -- 302 6052 0.1913 0.2074 -- 100.0
X Ray Diffraction 3.2092 3.5317 -- 312 6024 0.1693 0.1972 -- 100.0
X Ray Diffraction 3.5317 4.0418 -- 310 6023 0.1636 0.1789 -- 99.0
X Ray Diffraction 4.0418 5.0886 -- 321 6127 0.1523 0.177 -- 100.0
X Ray Diffraction 5.0886 30.987 -- 320 6188 0.2027 0.2009 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.346
f_plane_restr 0.007
f_chiral_restr 0.076
f_angle_d 1.384
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9086
Nucleic Acid Atoms 827
Heterogen Atoms 25
Solvent Atoms 1194

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