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Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP
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 B2: 30% (w/v) PEG 3350, 100 mM Hepes pH 7.5, 400 mM sodium chloride. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ added prior to crystallization, plate 14493 well B2 drop 1 , Puck: PSL1909, Cryo: 50% crystallant + 50% PEG 3350 (37.5% PEG 3350 total).
Crystal Properties Matthews coefficient Solvent content 2.5 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.195 α = 69.81 b = 68.048 β = 86.75 c = 84.274 γ = 85.57
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 47.66 97.2 0.111 0.133 0.071 0.981 6.2 3.5 91664
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 2.03 96.9 0.68 0.803 0.422 0.659 3.6
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 47.66 1.96 91654 4486 97.16 0.1694 0.1674 0.1798 0.2093 0.2173
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 14.551 f_angle_d 0.571 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9940 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 249
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing