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_plane_restr 0.007
f_angle_d 1.353
f_bond_d 0.011
f_chiral_restr 0.076
f_dihedral_angle_d 15.39
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

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