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Crystal structure of human 15-PGDH in complex with small molecule compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M NaI, 0.1M Bis-Tris Propane, pH 6.5, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.695 α = 90 b = 107.234 β = 98.564 c = 47.027 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 PILATUS3 S 6M 2022-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.180730 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.65 46.546 98.4 0.06 0.079 0.997 10.2 3.8 53999 17.239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99 0.408 0.535 0.821 2 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 46.546 53433 2680 97.356 0.193 0.1913 0.1908 0.2329 0.2334 24.289
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] -0.528 0.117 -0.357 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.259 r_dihedral_angle_6_deg 15.223 r_dihedral_angle_3_deg 12.608 r_lrange_it 6.181 r_dihedral_angle_1_deg 5.955 r_scangle_it 4.897 r_scbond_it 3.251 r_mcangle_it 2.487 r_angle_refined_deg 1.785 r_mcbond_it 1.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.259 r_dihedral_angle_6_deg 15.223 r_dihedral_angle_3_deg 12.608 r_lrange_it 6.181 r_dihedral_angle_1_deg 5.955 r_scangle_it 4.897 r_scbond_it 3.251 r_mcangle_it 2.487 r_angle_refined_deg 1.785 r_mcbond_it 1.782 r_nbtor_refined 0.321 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.154 r_chiral_restr 0.117 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3892 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing