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Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (P1 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Morpheus A1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag removed with 3C protease. 2mM methotrexate added to the protein prior to crystallization. Plate 14264 well A1 drop 2, Puck: PSL0116, Cryo: Direct.
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.356 α = 70.62 b = 67.806 β = 87.04 c = 84.762 γ = 84.65
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 2024-08-04 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 48.19 91.7 0.046 0.054 0.028 0.999 12.7 3.5 87261
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 2.04 96.6 0.628 0.738 0.383 0.793 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 48.19 1.97 87233 4385 91.65 0.2144 0.2124 0.2159 0.252 0.2529
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 14.186 f_angle_d 0.545 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 10004 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing