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Structure of AKR1C3 in complex with a bile acid fused tetrazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrochloride, and DL-serine; in 0.1 M bicine/Trizma base, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.02 39.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.462 α = 77.26 b = 51.413 β = 86.74 c = 77.879 γ = 77.63
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 PILATUS 6M 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.4 45.93 93.1 0.058 0.068 0.999 12.49 3.582 107028 21.72
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 1.4 1.48 92.7 0.582 0.679 0.828 2.13 3.638
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1ZQ5 1.4 45.93 105499 1533 93.12 0.155 0.1546 0.1547 0.1775 0.1777 RANDOM 17.31
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_4_deg 18.272 r_dihedral_angle_3_deg 12.705 r_dihedral_angle_1_deg 6.003 r_angle_other_deg 2.252 r_angle_refined_deg 1.743 r_chiral_restr 0.092 r_bond_other_d 0.034 r_gen_planes_other 0.015 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.746 r_dihedral_angle_4_deg 18.272 r_dihedral_angle_3_deg 12.705 r_dihedral_angle_1_deg 6.003 r_angle_other_deg 2.252 r_angle_refined_deg 1.743 r_chiral_restr 0.092 r_bond_other_d 0.034 r_gen_planes_other 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5072 Nucleic Acid Atoms Solvent Atoms 728 Heterogen Atoms 167
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction