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Crystal structures of prostaglandin D2 11-ketoreductase (AKR1C3) 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 1IHI
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 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.917 α = 90 b = 57.917 β = 90 c = 206.168 γ = 120
Symmetry Space Group P 32 2 1
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 210 2001-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.93 ESRF ID29
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 2 50 86.8 0.092 1.7 10 28450 24691 21.3
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 MOLECULAR REPLACEMENT THROUGHOUT 1IHI 2 48.8 23370 1184 100 0.15963 0.15774 0.1962 RANDOM 13.693
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] 0.91 0.45 0.91 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.935 r_scangle_it 2.635 r_scbond_it 1.55 r_angle_refined_deg 1.233 r_mcangle_it 0.958 r_angle_other_deg 0.797 r_mcbond_it 0.497 r_symmetry_vdw_other 0.255 r_nbd_other 0.231 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.935 r_scangle_it 2.635 r_scbond_it 1.55 r_angle_refined_deg 1.233 r_mcangle_it 0.958 r_angle_other_deg 0.797 r_mcbond_it 0.497 r_symmetry_vdw_other 0.255 r_nbd_other 0.231 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.152 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.126 r_nbtor_other 0.081 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing