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Crystal structure of ketosteroid isomerase M116A from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CPO PDB ENTRY 3CPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 298 1 M ammonium sulfate, 40 mM potassium phosphate pH 7.2, 1 mM EDTA, 2 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.82 α = 90 b = 94.723 β = 90 c = 72.391 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 ADSC QUANTUM 315r 2011-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.097 SSRL BL7-1
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 1.594 36.195 98 0.066 14.1 4 16562 16562
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 1.594 1.68 87.3 0.566 0.566 1.3 3.3
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 (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 3CPO 1.594 33.5 16532 15695 837 98.05 0.18098 0.17861 0.1831 0.22535 0.2291 RANDOM 15.736
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] 1.47 -0.99 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.648 r_dihedral_angle_4_deg 19.301 r_dihedral_angle_3_deg 15.777 r_dihedral_angle_1_deg 7.295 r_scangle_it 4.779 r_scbond_it 3.044 r_mcangle_it 2.157 r_angle_refined_deg 1.989 r_mcbond_it 1.299 r_angle_other_deg 1.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.648 r_dihedral_angle_4_deg 19.301 r_dihedral_angle_3_deg 15.777 r_dihedral_angle_1_deg 7.295 r_scangle_it 4.779 r_scbond_it 3.044 r_mcangle_it 2.157 r_angle_refined_deg 1.989 r_mcbond_it 1.299 r_angle_other_deg 1.063 r_mcbond_other 0.404 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction