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Crystal structure of human 15-PGDH in complex with small molecule compound 8b
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 7 277 60% v/v Tascimate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.84 56.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.71 α = 90 b = 82.71 β = 90 c = 161.88 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 PIXEL DECTRIS EIGER X 9M 2023-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98012 SOLEIL PROXIMA 2
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 1.88 65.503 99.9 0.162 0.169 0.999 15.7 21.5 27452 31.06
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 1.88 1.93 99.9 3.158 3.309 0.716 1.3 21.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.88 65.5 26026 1357 99.91 0.1816 0.17917 0.18 0.2303 0.2316 RANDOM 40.892
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] 1.19 0.59 1.19 -3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.664 r_dihedral_angle_3_deg 13.85 r_long_range_B_refined 9.387 r_dihedral_angle_1_deg 6.147 r_scbond_it 5.84 r_mcangle_it 4.894 r_mcbond_it 3.862 r_angle_refined_deg 1.805 r_chiral_restr 0.118 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.664 r_dihedral_angle_3_deg 13.85 r_long_range_B_refined 9.387 r_dihedral_angle_1_deg 6.147 r_scbond_it 5.84 r_mcangle_it 4.894 r_mcbond_it 3.862 r_angle_refined_deg 1.805 r_chiral_restr 0.118 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1974 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing