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Crystal Structure of Ketosteroid Isomerase D99N 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 8.5 298 2.0 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 4.17 70.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.357 α = 90 b = 104.786 β = 90 c = 141.435 γ = 90
Symmetry Space Group C 2 2 21
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 2010-03-24 SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-05-10 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 BL9-1 0.97946 SSRL BL9-1
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 1.966 29.309 99.4 0.092 13.9 4 32154 32154 34.805
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 1.966 2.07 97.1 0.613 0.613 1.2 3.3 4536
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 1.966 29.309 30919 30919 1565 95.39 0.2551 0.2551 0.2521 0.2501 0.3143 0.3122 RANDOM 27.8626
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] 10.25 8.82 -19.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_1_deg 3.629 r_angle_other_deg 1.835 r_angle_refined_deg 1.607 r_scangle_it 1.156 r_scbond_it 0.804 r_mcangle_it 0.465 r_mcbond_it 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 17.215 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_1_deg 3.629 r_angle_other_deg 1.835 r_angle_refined_deg 1.607 r_scangle_it 1.156 r_scbond_it 0.804 r_mcangle_it 0.465 r_mcbond_it 0.27 r_chiral_restr 0.088 r_mcbond_other 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1890 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 25
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