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Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JTV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 KH2PO4, PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.95 36.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.05 α = 90 b = 108.15 β = 90 c = 117.04 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2018-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.25 25 99.9 0.202 0.075 0.983 7.9 7.3 26759
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.37 100 0.509 0.185 0.932 7.4
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 1JTV 2.25 24.99 25322 1382 99.83 0.19316 0.18982 0.1971 0.25465 0.2648 RANDOM 39.441
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] 2.35 -3.81 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.04 r_dihedral_angle_2_deg 9.548 r_long_range_B_refined 8.68 r_long_range_B_other 8.679 r_dihedral_angle_1_deg 7.68 r_scangle_other 6.661 r_mcangle_other 5.163 r_mcangle_it 5.162 r_scbond_it 4.417 r_scbond_other 4.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.04 r_dihedral_angle_2_deg 9.548 r_long_range_B_refined 8.68 r_long_range_B_other 8.679 r_dihedral_angle_1_deg 7.68 r_scangle_other 6.661 r_mcangle_other 5.163 r_mcangle_it 5.162 r_scbond_it 4.417 r_scbond_other 4.416 r_mcbond_it 3.546 r_mcbond_other 3.546 r_angle_refined_deg 1.606 r_angle_other_deg 0.507 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 4248 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction