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 53% 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 = 93.81 α = 90
b = 109.22 β = 90
c = 150.58 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
1.6 50 92.1 0.045 -- -- 5.7 -- 187320 -- -3.0 27.797
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)
1.6 1.69 100.0 0.504 -- 3.61 -- --

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 1.6 30.062 -- 2.35 -- 179455 8168 88.24 -- 0.1719 0.1709 0.1941 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 1.6 1.6182 -- 289 5483 0.2346 0.2676 -- 86.0
X Ray Diffraction 1.6182 1.6372 -- 294 5582 0.225 0.26 -- 88.0
X Ray Diffraction 1.6372 1.6572 -- 300 5697 0.2139 0.2446 -- 89.0
X Ray Diffraction 1.6572 1.6782 -- 304 5788 0.2119 0.2553 -- 90.0
X Ray Diffraction 1.6782 1.7002 -- 303 5748 0.2007 0.2346 -- 91.0
X Ray Diffraction 1.7002 1.7235 -- 312 5938 0.1942 0.2383 -- 92.0
X Ray Diffraction 1.7235 1.7481 -- 313 5938 0.1887 0.231 -- 93.0
X Ray Diffraction 1.7481 1.7742 -- 315 5986 0.1874 0.2314 -- 93.0
X Ray Diffraction 1.7742 1.802 -- 317 6017 0.1801 0.2141 -- 94.0
X Ray Diffraction 1.802 1.8315 -- 317 6035 0.1791 0.2178 -- 95.0
X Ray Diffraction 1.8315 1.8631 -- 320 6070 0.1757 0.2077 -- 95.0
X Ray Diffraction 1.8631 1.8969 -- 258 4910 0.1758 0.2097 -- 87.0
X Ray Diffraction 1.9334 1.9729 -- 221 4196 0.1762 0.2379 -- 86.0
X Ray Diffraction 1.9729 2.0158 -- 232 6297 0.1708 0.1878 -- 97.0
X Ray Diffraction 2.0158 2.0627 -- 226 6434 0.1621 0.1822 -- 98.0
X Ray Diffraction 2.0627 2.1142 -- 245 6398 0.1579 0.1695 -- 99.0
X Ray Diffraction 2.1142 2.1714 -- 258 6390 0.1586 0.1812 -- 99.0
X Ray Diffraction 2.1714 2.2352 -- 244 5096 0.1592 0.169 -- 93.0
X Ray Diffraction 2.2352 2.3074 -- 84 2510 0.1581 0.1864 -- 88.0
X Ray Diffraction 2.3074 2.3898 -- 263 6457 0.1589 0.1826 -- 99.0
X Ray Diffraction 2.3898 2.4854 -- 258 6468 0.1629 0.1935 -- 99.0
X Ray Diffraction 2.4854 2.5985 -- 269 6453 0.1646 0.2005 -- 99.0
X Ray Diffraction 2.5985 2.7354 -- 279 6481 0.172 0.2034 -- 99.0
X Ray Diffraction 2.7354 2.9067 -- 292 6471 0.1769 0.2081 -- 99.0
X Ray Diffraction 2.9067 3.1309 -- 311 6491 0.1787 0.1908 -- 99.0
X Ray Diffraction 3.1309 3.4455 -- 337 6456 0.1657 0.1788 -- 99.0
X Ray Diffraction 3.4455 3.9432 -- 326 6386 0.1565 0.1748 -- 97.0
X Ray Diffraction 3.9432 4.9643 -- 339 6515 0.1456 0.1699 -- 99.0
X Ray Diffraction 4.9643 30.0675 -- 342 6596 0.1971 0.1995 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.39
f_plane_restr 0.007
f_chiral_restr 0.076
f_angle_d 1.353
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9294
Nucleic Acid Atoms 828
Heterogen Atoms 54
Solvent Atoms 1436

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