X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NT1PDB entry 3NT1, chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8291mCOX-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 Properties
Matthews coefficientSolvent content
2.8857.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.627α = 90
b = 133.538β = 90
c = 180.232γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4549.95498.90.1339.26.110695110695134.48
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5898.40.6540.6541.15.715407

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3NT1, chain A2.4549.9541.33106951106689533098.40.20320.20180.2306RANDOM34.2024
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.908
f_angle_d1.166
f_chiral_restr0.084
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17896
Nucleic Acid Atoms
Solvent Atoms1004
Heterogen Atoms528

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XSCALEdata scaling
PHASESphasing