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Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 UPH2O,3.5M Sodium formate pH7.0
Crystal Properties Matthews coefficient Solvent content 4.43 72.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.603 α = 90 b = 119.603 β = 90 c = 117.304 γ = 120
Symmetry Space Group P 31 1 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 PIXEL DECTRIS EIGER X 16M 2020-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 2.819 103.58 95.7 0.165 17.2 20.5 22365
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 2.82 2.97 1.341
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.819 77.764 22337 1135 95.703 0.191 0.1887 0.1889 0.2345 0.2348 64.51
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] 1.793 0.897 1.793 -5.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.177 r_dihedral_angle_4_deg 22.745 r_dihedral_angle_3_deg 18.07 r_lrange_other 11.302 r_lrange_it 11.296 r_scangle_it 8.742 r_scangle_other 8.74 r_mcangle_other 6.683 r_mcangle_it 6.682 r_dihedral_angle_1_deg 6.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.177 r_dihedral_angle_4_deg 22.745 r_dihedral_angle_3_deg 18.07 r_lrange_other 11.302 r_lrange_it 11.296 r_scangle_it 8.742 r_scangle_other 8.74 r_mcangle_other 6.683 r_mcangle_it 6.682 r_dihedral_angle_1_deg 6.434 r_scbond_it 6.046 r_scbond_other 6.044 r_mcbond_it 4.72 r_mcbond_other 4.711 r_angle_other_deg 2.43 r_angle_refined_deg 1.557 r_nbd_other 0.259 r_symmetry_nbd_refined 0.257 r_symmetry_nbd_other 0.233 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.066 r_bond_other_d 0.037 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3842 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing