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 MnSO4, 100mM MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.18 α = 90
b = 108.59 β = 90
c = 150.99 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
1.65 50 98.2 0.109 -- -- 10.0 -- 180667 -- -3.0 29.445
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)
1.65 1.75 89.1 0.509 -- 3.72 -- --

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 1.651 34.19 -- 2.35 -- 175745 7731 95.78 -- 0.1751 0.174 0.1994 Inherited free reflections from 4F2R
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 1.6511 1.6699 -- 120 2414 0.2834 0.2956 -- 42.0
X Ray Diffraction 1.6699 1.6895 -- 255 5243 0.2301 0.2588 -- 90.0
X Ray Diffraction 1.6895 1.7101 -- 260 5285 0.2208 0.2552 -- 92.0
X Ray Diffraction 1.7101 1.7318 -- 264 5348 0.2142 0.2316 -- 93.0
X Ray Diffraction 1.7318 1.7546 -- 268 5411 0.2141 0.2754 -- 94.0
X Ray Diffraction 1.7546 1.7786 -- 268 5449 0.2037 0.2243 -- 94.0
X Ray Diffraction 1.7786 1.804 -- 283 5493 0.1971 0.2233 -- 95.0
X Ray Diffraction 1.804 1.8309 -- 283 5485 0.2042 0.2304 -- 95.0
X Ray Diffraction 1.8309 1.8596 -- 276 5566 0.2002 0.2372 -- 96.0
X Ray Diffraction 1.8596 1.89 -- 285 5543 0.1893 0.2297 -- 96.0
X Ray Diffraction 1.89 1.9226 -- 291 5592 0.1835 0.2337 -- 97.0
X Ray Diffraction 1.9226 1.9576 -- 289 5668 0.1818 0.2156 -- 98.0
X Ray Diffraction 1.9576 1.9952 -- 199 5759 0.1757 0.1902 -- 98.0
X Ray Diffraction 1.9952 2.036 -- 207 5790 0.1735 0.2173 -- 99.0
X Ray Diffraction 2.036 2.0802 -- 210 5776 0.1718 0.1852 -- 99.0
X Ray Diffraction 2.0802 2.1286 -- 234 5818 0.1686 0.2093 -- 99.0
X Ray Diffraction 2.1286 2.1818 -- 223 5812 0.1644 0.1945 -- 99.0
X Ray Diffraction 2.1818 2.2408 -- 273 5771 0.1658 0.1947 -- 99.0
X Ray Diffraction 2.2408 2.3067 -- 213 5882 0.1589 0.2018 -- 100.0
X Ray Diffraction 2.3067 2.3812 -- 229 5821 0.1594 0.1912 -- 99.0
X Ray Diffraction 2.3812 2.4662 -- 245 5850 0.1635 0.1971 -- 100.0
X Ray Diffraction 2.4662 2.565 -- 232 5877 0.1662 0.1846 -- 100.0
X Ray Diffraction 2.565 2.6817 -- 252 5835 0.1743 0.1945 -- 100.0
X Ray Diffraction 2.6817 2.823 -- 258 5871 0.1812 0.2224 -- 100.0
X Ray Diffraction 2.823 2.9997 -- 287 5877 0.1861 0.2255 -- 100.0
X Ray Diffraction 2.9997 3.2312 -- 294 5855 0.1826 0.1961 -- 100.0
X Ray Diffraction 3.2312 3.5561 -- 306 5866 0.1662 0.1898 -- 100.0
X Ray Diffraction 3.5561 4.0699 -- 299 5933 0.1541 0.1683 -- 100.0
X Ray Diffraction 4.0699 5.1249 -- 312 5952 0.1464 0.1685 -- 100.0
X Ray Diffraction 5.1249 34.1972 -- 316 6172 0.1918 0.2018 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.293
f_plane_restr 0.007
f_chiral_restr 0.094
f_angle_d 1.403
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 110
Solvent Atoms 1323

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