X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 180.71 α = 90
b = 133.94 β = 90
c = 122.22 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-01-31
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C -- APS 24-ID-C

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
2.11 50.11 99.7 0.078 0.035 -- 6.8 -- 170000 -- 0.0 29.46
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)
2.11 2.22 99.5 0.561 0.248 3.5 6.9 --

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
MOLECULAR REPLACEMENT 2.11 50.11 -- 1.35 170113 169740 5131 99.5 -- 0.177 0.177 0.199 --
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 2.1093 2.1333 -- 151 5396 0.231 0.2867 -- 98.0
X Ray Diffraction 2.1333 2.1584 -- 168 5412 0.2281 0.271 -- 99.0
X Ray Diffraction 2.1584 2.1847 -- 179 5446 0.2202 0.2676 -- 100.0
X Ray Diffraction 2.1847 2.2123 -- 163 5391 0.2132 0.2619 -- 100.0
X Ray Diffraction 2.2123 2.2414 -- 164 5474 0.2211 0.241 -- 100.0
X Ray Diffraction 2.2414 2.2721 -- 162 5467 0.2093 0.2459 -- 99.0
X Ray Diffraction 2.2721 2.3046 -- 174 5426 0.1996 0.2302 -- 100.0
X Ray Diffraction 2.3046 2.339 -- 155 5446 0.2021 0.2691 -- 100.0
X Ray Diffraction 2.339 2.3756 -- 142 5485 0.191 0.2397 -- 100.0
X Ray Diffraction 2.3756 2.4145 -- 174 5461 0.1865 0.2315 -- 100.0
X Ray Diffraction 2.4145 2.4561 -- 177 5430 0.1873 0.2142 -- 100.0
X Ray Diffraction 2.4561 2.5008 -- 179 5475 0.1869 0.2269 -- 100.0
X Ray Diffraction 2.5008 2.5489 -- 173 5431 0.1827 0.1991 -- 99.0
X Ray Diffraction 2.5489 2.6009 -- 160 5477 0.1884 0.2253 -- 100.0
X Ray Diffraction 2.6009 2.6575 -- 173 5483 0.1825 0.2098 -- 100.0
X Ray Diffraction 2.6575 2.7193 -- 176 5457 0.1779 0.2226 -- 100.0
X Ray Diffraction 2.7193 2.7873 -- 177 5506 0.1803 0.2047 -- 100.0
X Ray Diffraction 2.7873 2.8626 -- 154 5437 0.1828 0.2132 -- 100.0
X Ray Diffraction 2.8626 2.9469 -- 189 5495 0.1824 0.2213 -- 100.0
X Ray Diffraction 2.9469 3.042 -- 171 5487 0.187 0.2266 -- 100.0
X Ray Diffraction 3.042 3.1507 -- 173 5486 0.1901 0.2168 -- 100.0
X Ray Diffraction 3.1507 3.2768 -- 169 5524 0.1805 0.2017 -- 100.0
X Ray Diffraction 3.2768 3.4259 -- 194 5456 0.1858 0.2036 -- 99.0
X Ray Diffraction 3.4259 3.6065 -- 174 5496 0.1687 0.1874 -- 100.0
X Ray Diffraction 3.6065 3.8323 -- 184 5536 0.158 0.1858 -- 100.0
X Ray Diffraction 3.8323 4.1281 -- 183 5519 0.1505 0.154 -- 100.0
X Ray Diffraction 4.1281 4.5433 -- 171 5572 0.141 0.1456 -- 100.0
X Ray Diffraction 4.5433 5.2001 -- 181 5502 0.1432 0.1498 -- 99.0
X Ray Diffraction 5.2001 6.5493 -- 170 5646 0.1795 0.2112 -- 100.0
X Ray Diffraction 6.5493 50.1224 -- 171 5790 0.1801 0.1715 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.363
f_bond_d 0.007
f_plane_restr 0.008
f_dihedral_angle_d 13.644
f_chiral_restr 0.078
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17878
Nucleic Acid Atoms 0
Heterogen Atoms 700
Solvent Atoms 1531

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASES phasing
PHENIX refinement version: (phenix.refine: 1.8.4_1496)
XDS data reduction
SCALEPACK data scaling