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Crystal Structure of Ketosteroid Isomerase D99N 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 3M8C PDB ENTRY 3M8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 2 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 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.28 α = 90 b = 61.28 β = 90 c = 142.861 γ = 120
Symmetry Space Group P 65 2 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 1.59 28.572 100 0.072 19.9 13.7 22234 21.8
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 1.59 1.68 100 0.744 0.744 1 14
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 3M8C 1.59 28.57 22163 22163 1133 100 0.185 0.183 0.219 0.2181 RANDOM 24.05
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] 0.51 0.26 0.51 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.436 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 6.392 r_scangle_it 5.548 r_scbond_it 3.832 r_angle_refined_deg 2.615 r_mcangle_it 2.394 r_mcbond_it 1.548 r_chiral_restr 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.436 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 6.392 r_scangle_it 5.548 r_scbond_it 3.832 r_angle_refined_deg 2.615 r_mcangle_it 2.394 r_mcbond_it 1.548 r_chiral_restr 0.205 r_bond_refined_d 0.032 r_gen_planes_refined 0.017 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 945 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 71
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction