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The X-ray structure of 7beta-hydroxysteroid dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M Sodium malonate pH 7.0, 12% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.73 α = 90 b = 72.73 β = 90 c = 171.31 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 315r 2016-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97911 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 99.4 13.7 6.5 51175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 5FYD 1.7 44.91 48520 2566 99.2 0.167 0.165 0.1766 0.201 0.2101 RANDOM 16.88
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.784 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 15.099 r_dihedral_angle_1_deg 6.625 r_long_range_B_refined 5.509 r_long_range_B_other 5.506 r_scangle_other 4.398 r_scbond_it 2.921 r_scbond_other 2.921 r_mcangle_it 2.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.784 r_dihedral_angle_4_deg 16.52 r_dihedral_angle_3_deg 15.099 r_dihedral_angle_1_deg 6.625 r_long_range_B_refined 5.509 r_long_range_B_other 5.506 r_scangle_other 4.398 r_scbond_it 2.921 r_scbond_other 2.921 r_mcangle_it 2.474 r_mcangle_other 2.473 r_angle_refined_deg 1.809 r_mcbond_it 1.723 r_mcbond_other 1.721 r_angle_other_deg 0.843 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4019 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement iMOSFLM data processing