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Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
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 289.15 0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph 6.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 4.43 72.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.89 α = 90 b = 118.89 β = 90 c = 118.61 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 2.3 102.96 99.7 0.019 19.3 20.7 42673
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 2.34 2.47 1.292
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 (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 FREE R-VALUE 2.3 29.7 40509 2164 99.92 0.19324 0.19166 0.2002 0.22291 0.2283 RANDOM 53.403
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] 1.17 0.59 1.17 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_4_deg 21.129 r_dihedral_angle_3_deg 16.741 r_long_range_B_refined 13.369 r_long_range_B_other 13.368 r_scangle_other 9.033 r_dihedral_angle_1_deg 6.874 r_scbond_it 6.623 r_scbond_other 6.622 r_mcangle_it 5.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_4_deg 21.129 r_dihedral_angle_3_deg 16.741 r_long_range_B_refined 13.369 r_long_range_B_other 13.368 r_scangle_other 9.033 r_dihedral_angle_1_deg 6.874 r_scbond_it 6.623 r_scbond_other 6.622 r_mcangle_it 5.975 r_mcangle_other 5.974 r_mcbond_it 4.688 r_mcbond_other 4.669 r_angle_other_deg 2.459 r_angle_refined_deg 1.716 r_chiral_restr 0.093 r_bond_other_d 0.037 r_gen_planes_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3842 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing