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Crystal structure of ketosteroid isomerase D38ND99N from Pseudomonas testosteroni (tKSI) with 4-Androstene-3,17-dione Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CHO PDB ENTRY 8CHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 1.8 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.785 α = 90 b = 59.785 β = 90 c = 144.499 γ = 120
Symmetry Space Group P 32 1 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 CCD MARMOSAIC 325 mm CCD 2010-03-25 SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2010-03-24 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.758 29.627 99 0.096 12.1 6.6 29522 24.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.758 1.85 93.7 0.01 1.047 0.5 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 8CHO 1.76 29.627 29405 29405 1499 99 0.177 0.176 0.198 0.1974 RANDOM 27.91
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] 0.86 0.86 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.089 r_dihedral_angle_4_deg 19.797 r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 6.828 r_scangle_it 4.063 r_scbond_it 2.758 r_angle_refined_deg 1.826 r_mcangle_it 1.675 r_mcbond_it 0.998 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.089 r_dihedral_angle_4_deg 19.797 r_dihedral_angle_3_deg 16.4 r_dihedral_angle_1_deg 6.828 r_scangle_it 4.063 r_scbond_it 2.758 r_angle_refined_deg 1.826 r_mcangle_it 1.675 r_mcbond_it 0.998 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 66
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing