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Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 protein was incubated at 12 mg/ml with 1 mM NAD+ and 1 mM compound 1 with the addition of 0.125% beta-octyl-glucoside. Sitting drop vapor diffusion crystallization was set up by mixing 300 nl protein complex with 300 nl of reservoir solution containing 30% PEG3350, 0.2 M ammonium chloride. Crystals grew at room temperature over 2 weeks.
Crystal Properties Matthews coefficient Solvent content 3.27 62.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.97 α = 90 b = 76.06 β = 94.69 c = 65.24 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2020-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.09 93.17 87.9 0.059 0.038 0.998 11.9 3.3 28362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.36 56.2 0.359 0.33 0.763 2 1.9
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 2.09 33.47 28372 1410 46.5 0.2126 0.2113 0.2064 0.2393 0.2329 RANDOM 45.53
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] 5.9579 0.3583 0.9125 -6.8704
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.34 t_omega_torsion 3.2 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3940 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 132
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction STARANISO data scaling PHASER phasing