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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 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.808 α = 90 b = 63.074 β = 90 c = 96.2 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 1.7 52.7 98 0.049 18.7 3.4 38057 37296 16.54
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) 1.7 1.79 88.3 0.2 4.7 2.7 5420
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 1.7 20 35385 1860 97.79 0.17356 0.17227 0.19838 RANDOM 23.7
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] 0.33 0.27 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.619 r_scangle_it 3.223 r_scbond_it 1.936 r_angle_refined_deg 1.602 r_angle_other_deg 1.423 r_mcangle_it 1.18 r_mcbond_it 0.59 r_symmetry_vdw_other 0.299 r_symmetry_hbond_refined 0.29 r_symmetry_vdw_refined 0.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.619 r_scangle_it 3.223 r_scbond_it 1.936 r_angle_refined_deg 1.602 r_angle_other_deg 1.423 r_mcangle_it 1.18 r_mcbond_it 0.59 r_symmetry_vdw_other 0.299 r_symmetry_hbond_refined 0.29 r_symmetry_vdw_refined 0.265 r_nbd_other 0.232 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.163 r_nbtor_other 0.086 r_chiral_restr 0.076 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2524 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing