☰ Navigation Tabs
Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 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 7 291 1.8 M Ammonium citrate tribasic, pH7.0
Crystal Properties Matthews coefficient Solvent content 4.5 72.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.108 α = 90 b = 120.108 β = 90 c = 117.242 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) CC (Half) 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 2.079 104.234 100 1 16.2 10.5 58119
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.14 0.858
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 2.079 104.234 58114 2850 99.923 0.196 0.1944 0.1951 0.2286 0.2298 41.679
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] 0.813 0.407 0.813 -2.637
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.662 r_dihedral_angle_4_deg 21.173 r_dihedral_angle_3_deg 15.645 r_lrange_other 7.884 r_lrange_it 7.878 r_scangle_it 7.735 r_scangle_other 7.733 r_dihedral_angle_1_deg 6.626 r_scbond_it 5.801 r_scbond_other 5.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.662 r_dihedral_angle_4_deg 21.173 r_dihedral_angle_3_deg 15.645 r_lrange_other 7.884 r_lrange_it 7.878 r_scangle_it 7.735 r_scangle_other 7.733 r_dihedral_angle_1_deg 6.626 r_scbond_it 5.801 r_scbond_other 5.8 r_mcangle_it 4.728 r_mcangle_other 4.727 r_mcbond_it 3.665 r_mcbond_other 3.665 r_angle_other_deg 2.442 r_angle_refined_deg 1.762 r_nbd_other 0.409 r_symmetry_nbd_refined 0.391 r_symmetry_nbd_other 0.218 r_nbd_refined 0.214 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.037 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3812 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing