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Crystal structure of Ketosteroid Isomerase D38HD99N 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 sitting drop 7.2 298 1.2 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2mM DTT, 1.8mM equilenin, pH 7.2, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.274 α = 90 b = 64.274 β = 90 c = 504.199 γ = 120
Symmetry Space Group P 61 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 2010-01-05 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 1.961 29.348 98.6 0.142 14 11.7 45766 45766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.961 2.07 91.1 0.802 0.802 0.87 0.31 1 6.8 5946
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 8CHO 1.961 29.34 41851 2219 95.17 0.2262 0.22336 0.2229 0.28184 0.2809 RANDOM 24.452
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] 0.9 0.45 0.9 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.005 r_dihedral_angle_4_deg 19.239 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_1_deg 6.695 r_scangle_it 4.725 r_scbond_it 3.17 r_mcangle_it 2.06 r_angle_refined_deg 2.049 r_mcbond_it 1.231 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.005 r_dihedral_angle_4_deg 19.239 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_1_deg 6.695 r_scangle_it 4.725 r_scbond_it 3.17 r_mcangle_it 2.06 r_angle_refined_deg 2.049 r_mcbond_it 1.231 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 3776 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 159
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