☰ Navigation Tabs
Crystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with NADP(H), citrate and acetate molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J96 PDB ENTRY 1J96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.7 293 Sodium citrate, PEG4000, Lithium sulfate, pH 5.7, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.12 α = 90 b = 143.12 β = 90 c = 204.31 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS II monochromator 2001-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 19.17 0.085 0.063 17.8 4.7 59186 56866 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 88.9 0.375 0.466 3.4 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1J96 1.9 19.17 56866 56866 3003 100 0.17486 0.17361 0.1793 0.19855 0.1928 RANDOM 32.498
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 15.872 r_dihedral_angle_3_deg 11.878 r_dihedral_angle_1_deg 9.25 r_scangle_it 4.459 r_scbond_it 3.523 r_mcangle_it 2.152 r_angle_refined_deg 2.027 r_mcbond_it 1.711 r_nbd_refined 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 15.872 r_dihedral_angle_3_deg 11.878 r_dihedral_angle_1_deg 9.25 r_scangle_it 4.459 r_scbond_it 3.523 r_mcangle_it 2.152 r_angle_refined_deg 2.027 r_mcbond_it 1.711 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.151 r_symmetry_hbond_refined 0.135 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5183 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction AMoRE phasing CNS refinement Crystal data collection CrystalClear data reduction XDS data scaling