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X-ray structure of 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 30% Polyethylene glycol monomethyl ether 550,0.1M Bis-Tris pH7.0,0.05M Magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.44 49.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.496 α = 90 b = 79.538 β = 90 c = 114.365 γ = 90
Symmetry Space Group I 2 2 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 2023-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
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 1.198 57.18 87.6 0.046 19.1 5.4 69742
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 1.2 1.26 0.258
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.2 45.55 66233 3501 87.5 0.167 0.16699 0.16632 0.17936 0.1999 RANDOM 11.513
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] 0.1 0.41 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 17.505 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.606 r_long_range_B_refined 3.31 r_long_range_B_other 3.253 r_scangle_other 2.943 r_angle_other_deg 2.524 r_scbond_other 2.354 r_scbond_it 2.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_4_deg 17.505 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.606 r_long_range_B_refined 3.31 r_long_range_B_other 3.253 r_scangle_other 2.943 r_angle_other_deg 2.524 r_scbond_other 2.354 r_scbond_it 2.353 r_angle_refined_deg 2.109 r_mcangle_it 1.246 r_mcangle_other 1.246 r_mcbond_it 0.905 r_mcbond_other 0.904 r_chiral_restr 0.107 r_bond_other_d 0.037 r_bond_refined_d 0.023 r_gen_planes_refined 0.016 r_gen_planes_other 0.015 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 1818 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing