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Crystal structures of prostaglandin D2 11-ketoreductase in complex with the non-steroidal anti-inflammatory drugs flufenamic acid and indomethacin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.23 44.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.798 α = 90 b = 63 β = 90 c = 96.289 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2002-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 52.7 99.7 0.078 13.6 4.4 32180 32084 17.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 98.1 0.256 3.8 2.8 4459
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION isomorphous replacement THROUGHOUT 1S1P 1.8 48 30396 1634 99.63 0.16996 0.16814 0.20491 RANDOM 19.2
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] 0.88 -0.24 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.503 r_scangle_it 2.649 r_scbond_it 1.593 r_angle_refined_deg 1.239 r_angle_other_deg 1.139 r_mcangle_it 1.021 r_mcbond_it 0.512 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_other 0.259 r_nbd_other 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.503 r_scangle_it 2.649 r_scbond_it 1.593 r_angle_refined_deg 1.239 r_angle_other_deg 1.139 r_mcangle_it 1.021 r_mcbond_it 0.512 r_symmetry_hbond_refined 0.276 r_symmetry_vdw_other 0.259 r_nbd_other 0.227 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.139 r_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing