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 47%-49% 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 = 93.22 α = 90
b = 108.48 β = 90
c = 150.95 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-10-30
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
1.63 50 100.0 0.063 -- -- 10.0 -- 190429 -- -3.0 29.124
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)
1.63 1.73 99.8 0.506 -- 3.38 -- --

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 1.63 34.98 -- 2.35 -- 184317 8311 96.77 -- 0.1708 0.1698 0.1924 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 1.63 1.6485 -- 267 5062 0.2473 0.266 -- 85.0
X Ray Diffraction 1.6485 1.6679 -- 278 5282 0.2354 0.2498 -- 88.0
X Ray Diffraction 1.6679 1.6883 -- 281 5334 0.2233 0.2535 -- 89.0
X Ray Diffraction 1.6883 1.7096 -- 285 5421 0.2183 0.2497 -- 91.0
X Ray Diffraction 1.7096 1.7321 -- 287 5464 0.2039 0.2441 -- 91.0
X Ray Diffraction 1.7321 1.7559 -- 296 5619 0.2013 0.2299 -- 93.0
X Ray Diffraction 1.7559 1.7809 -- 295 5609 0.1936 0.2378 -- 94.0
X Ray Diffraction 1.7809 1.8075 -- 302 5723 0.1865 0.2085 -- 95.0
X Ray Diffraction 1.8075 1.8358 -- 300 5711 0.1862 0.2202 -- 95.0
X Ray Diffraction 1.8358 1.8659 -- 301 5724 0.1866 0.2314 -- 96.0
X Ray Diffraction 1.8659 1.898 -- 303 5750 0.1835 0.2173 -- 96.0
X Ray Diffraction 1.898 1.9325 -- 309 5861 0.1777 0.2058 -- 98.0
X Ray Diffraction 1.9325 1.9697 -- 307 5839 0.1786 0.2199 -- 98.0
X Ray Diffraction 1.9697 2.0099 -- 182 6025 0.1745 0.2114 -- 98.0
X Ray Diffraction 2.0099 2.0536 -- 212 6037 0.1667 0.1802 -- 99.0
X Ray Diffraction 2.0536 2.1014 -- 231 6035 0.1657 0.1995 -- 99.0
X Ray Diffraction 2.1014 2.1539 -- 247 6018 0.1609 0.178 -- 99.0
X Ray Diffraction 2.1539 2.2121 -- 264 6056 0.1598 0.1908 -- 99.0
X Ray Diffraction 2.2121 2.2772 -- 238 6041 0.1599 0.1895 -- 99.0
X Ray Diffraction 2.2772 2.3507 -- 227 6074 0.1538 0.1947 -- 99.0
X Ray Diffraction 2.3507 2.4347 -- 250 6061 0.1607 0.1851 -- 100.0
X Ray Diffraction 2.4347 2.5322 -- 253 6089 0.1618 0.1882 -- 100.0
X Ray Diffraction 2.5322 2.6474 -- 254 6100 0.1698 0.1766 -- 100.0
X Ray Diffraction 2.6474 2.7869 -- 271 6075 0.1749 0.2031 -- 100.0
X Ray Diffraction 2.7869 2.9614 -- 284 6090 0.1857 0.2282 -- 100.0
X Ray Diffraction 2.9614 3.1899 -- 304 6096 0.1797 0.1971 -- 100.0
X Ray Diffraction 3.1899 3.5107 -- 318 6085 0.1591 0.1716 -- 100.0
X Ray Diffraction 3.5107 4.018 -- 314 6139 0.1487 0.1536 -- 100.0
X Ray Diffraction 4.018 5.0599 -- 321 6197 0.1413 0.1634 -- 100.0
X Ray Diffraction 5.0599 34.988 -- 330 6389 0.1864 0.1996 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.169
f_plane_restr 0.007
f_chiral_restr 0.083
f_angle_d 1.375
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9310
Nucleic Acid Atoms 832
Heterogen Atoms 120
Solvent Atoms 1238

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