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Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 2,6-difluorophenol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B32 PDB entry 2B32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Ammonium sulphate 1.4 M, 2-propanol 6.5%
protein concentration 25 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.114 α = 90 b = 94.887 β = 90 c = 72.424 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 110 CCD ADSC QUANTUM 315 2004-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 APS 14-BM-C
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 1.5 47.4 96.8 0.079 16.1 9 19911 19274 -3 24.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.55 96.7 0.374 4.4 8.9 1890
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 2B32 1.5 47.4 18650 1830 93.69 0.19 0.185 0.1889 0.234 0.2416 RANDOM 26.929
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] 2.88 -2.58 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.808 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 13.768 r_sphericity_free 11.133 r_sphericity_bonded 6.452 r_dihedral_angle_1_deg 5.874 r_scangle_it 5.5 r_scbond_it 3.957 r_mcangle_it 3.285 r_rigid_bond_restr 2.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.808 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 13.768 r_sphericity_free 11.133 r_sphericity_bonded 6.452 r_dihedral_angle_1_deg 5.874 r_scangle_it 5.5 r_scbond_it 3.957 r_mcangle_it 3.285 r_rigid_bond_restr 2.575 r_mcbond_it 2.266 r_angle_refined_deg 1.906 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.19 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.13 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1020 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing