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Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin
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 C9: 25% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ and 2mM indomethacin addied prior to crystallization, plate 14493 well C9 drop 2 , Puck: PSL1906, Cryo: 50% crystallant + 50% PEG 3350 (37.5% PEG 3350 total).
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.822 α = 90 b = 94.72 β = 94.88 c = 87.332 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER2 XE 9M 2024-10-24 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 2.1 49.59 99.9 0.202 0.222 0.09 0.991 8.7 6.1 80333
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 2.1 2.14 99.9 1.323 1.444 0.574 0.533 6.3
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 2.1 47.36 1.34 80287 3922 99.85 0.2016 0.1998 0.2046 0.2362 0.2385
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 13.362 f_angle_d 0.557 f_chiral_restr 0.042 f_plane_restr 0.008 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10008 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 302
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing