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Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13
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 25% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.75 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.15 α = 90 b = 161.56 β = 95.05 c = 100.77 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 EIGER X 16M 2020-03-12 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 2.645 90.95 93.4 0.083 0.99 7.9 3.4 67940
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 2.645 2.897 0.589 0.462 1.5
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 2.645 37.91 67909 3399 76.1 0.2136 0.212 0.2091 0.2443 0.2431 RANDOM 61.47
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] -0.6003 1.2256 -0.6366 1.2369
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.08 t_omega_torsion 2.71 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.08 t_omega_torsion 2.71 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17326 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 777
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling PHASER phasing