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Crystal structure of ketosteroid isomerase Y16AD103A from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 1.6 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.514 α = 90 b = 76.644 β = 63.96 c = 53.06 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2011-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.980 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 1.465 38.322 98 0.038 18 3.6 77168 77168
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 1.46 1.54 88.4 0.872 0.872 0.9 3.2 10103
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3RGR 1.47 38.32 1 77108 77108 3852 97.97 0.1876 0.1876 0.1859 0.1924 0.2181 0.2194 RANDOM 27.0688
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] -0.1 -0.18 0.8 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_3_deg 15.354 r_dihedral_angle_4_deg 14.645 r_dihedral_angle_1_deg 6.12 r_scangle_it 3.719 r_scbond_it 2.354 r_mcangle_it 1.652 r_angle_refined_deg 1.521 r_angle_other_deg 0.934 r_mcbond_it 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.33 r_dihedral_angle_3_deg 15.354 r_dihedral_angle_4_deg 14.645 r_dihedral_angle_1_deg 6.12 r_scangle_it 3.719 r_scbond_it 2.354 r_mcangle_it 1.652 r_angle_refined_deg 1.521 r_angle_other_deg 0.934 r_mcbond_it 0.934 r_mcbond_other 0.256 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3955 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 45
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction