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Crystal structure of AKR1B10 in complex with NADP+ and Androst-4-ene-3-beta-6-alpha-diol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 289 100mM Tris, 30-35% PEG 6000, 3-5% 1,6-Hexanediol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.864 α = 90 b = 89.864 β = 90 c = 78.309 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 CCD OXFORD ONYX CCD 2014-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
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 2.5 25.94 99.87 0.111 12.7 6.1 12535
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 2.5 2.64 100 0.518 6.1
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 4JIH 2.5 25.94 11882 632 99.87 0.18112 0.17789 0.1896 0.24471 0.248 RANDOM 31.637
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 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.578 r_dihedral_angle_3_deg 16.571 r_dihedral_angle_4_deg 10.451 r_dihedral_angle_1_deg 6.683 r_long_range_B_refined 6.038 r_long_range_B_other 5.995 r_scangle_other 4.004 r_mcangle_it 3.98 r_mcangle_other 3.98 r_mcbond_it 2.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.578 r_dihedral_angle_3_deg 16.571 r_dihedral_angle_4_deg 10.451 r_dihedral_angle_1_deg 6.683 r_long_range_B_refined 6.038 r_long_range_B_other 5.995 r_scangle_other 4.004 r_mcangle_it 3.98 r_mcangle_other 3.98 r_mcbond_it 2.518 r_mcbond_other 2.517 r_scbond_it 2.475 r_scbond_other 2.474 r_angle_refined_deg 1.867 r_angle_other_deg 0.871 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 2525 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling CrysalisPro data collection MOLREP phasing