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Crystal Structure of Ketosteroid Isomerase D40N-D103N from Pseudomonas putida (pKSI) with bound equilenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2INX PDB ENTRY 2INX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 Ammonium sulphate 1.4 M, 2-propanol 6.5%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.876 α = 90 b = 71.196 β = 89.92 c = 50.452 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 315 2007-02-24 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.32 50 94 0.088 10.337 2.9 68149 68149 -3 -3 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.37 70.2 0.373 2.2 5090
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 2INX 1.32 55.05 68136 68136 3452 93.76 0.151 0.151 0.149 0.1535 0.183 0.1892 RANDOM 19.12
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] 1.56 0.51 -0.24 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.728 r_dihedral_angle_4_deg 20.791 r_dihedral_angle_3_deg 13.931 r_sphericity_free 8.979 r_dihedral_angle_1_deg 5.8 r_sphericity_bonded 5.089 r_scangle_it 4.486 r_mcangle_it 3.685 r_scbond_it 3.355 r_mcbond_it 3.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.728 r_dihedral_angle_4_deg 20.791 r_dihedral_angle_3_deg 13.931 r_sphericity_free 8.979 r_dihedral_angle_1_deg 5.8 r_sphericity_bonded 5.089 r_scangle_it 4.486 r_mcangle_it 3.685 r_scbond_it 3.355 r_mcbond_it 3.016 r_rigid_bond_restr 2.662 r_angle_refined_deg 2.126 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.315 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.153 r_bond_refined_d 0.023 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1971 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection