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Crystal structures of HSD17B13 complexes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG3350, 0.2 M ammonium chloride
Crystal Properties Matthews coefficient Solvent content 3.52 65.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.379 α = 90 b = 187.205 β = 90 c = 65.365 γ = 90
Symmetry Space Group P 21 21 2
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 2019-10-23 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) 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 2.467 93.6 93.7 0.077 0.996 8.3 6.6 29109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.467 2.64 50.6 0.579 0.581 6.8
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 2.467 24.16 29060 1447 84.1 0.2011 0.1997 0.1948 0.2274 0.2191 RANDOM 56.42
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] 2.6476 -0.0014 -2.6462
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.44 t_omega_torsion 3.05 t_angle_deg 0.89 t_bond_d 0.007 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 4678 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 88
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling PHASER phasing