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Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin (Orthorhombic P form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9D6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Berkeley C1: 25% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM ammonium sulfate. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ addied prior to crystallization and crystals were soaked for 24 hours in 5mM IMN in crystallant, plate 14493 well C1 drop 1 , Puck: PSL1004, Cryo: 80% crystallant + 20% PEG 200.
Crystal Properties Matthews coefficient Solvent content 2.88 57.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.535 α = 90 b = 98.675 β = 90 c = 181.622 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 PIXEL DECTRIS EIGER2 XE 9M 2024-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 47.61 100 0.097 0.101 0.028 0.999 15.6 13.2 74640
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.35 100 1.576 1.639 0.446 0.773 13.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 47.61 1.34 74528 3702 99.94 0.2026 0.2006 0.2032 0.2397 0.2401
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 Key Refinement Restraint Deviation f_dihedral_angle_d 13.208 f_angle_d 0.623 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9998 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 365
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing