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_angle_d 1.384
f_plane_restr 0.007
f_chiral_restr 0.076
f_bond_d 0.011
f_dihedral_angle_d 15.346
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

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