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Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI)
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 VAPOR DIFFUSION, SITTING DROP 7 298 2.0 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.356 α = 90 b = 59.356 β = 90 c = 141.974 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 0.97946 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 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 1.887 29.678 99.6 0.078 21.6 13.2 12614 12614 29.1
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 1.887 1.99 97.2 0.983 0.983 0.8 10.8 1741
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 (All) 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 PDB ENTRY 8CHO 1.887 29.678 12563 12563 610 99.53 0.2048 0.2048 0.2024 0.2079 0.2536 0.2633 RANDOM 37.019
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] 1.41 0.71 1.41 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 17.854 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.952 r_scangle_it 6.085 r_scbond_it 3.858 r_mcangle_it 2.301 r_angle_refined_deg 2.137 r_mcbond_it 1.39 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 17.854 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.952 r_scangle_it 6.085 r_scbond_it 3.858 r_mcangle_it 2.301 r_angle_refined_deg 2.137 r_mcbond_it 1.39 r_chiral_restr 0.152 r_bond_refined_d 0.026 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 938 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection Web-Ice data collection XDS data reduction