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Crystal Structure of AKR1C1 complexed with glibenclamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 289 23-27% (w/v) PEG 4000, 100 mM Hepes, 10mM CaCl2, 0.4M NaCl
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.545 α = 90 b = 76.168 β = 94.88 c = 88.706 γ = 90
Symmetry Space Group P 1 21 1
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 OXFORD ONYX CCD 2014-08-27 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) Rrim I (All) Rpim I (All) 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 2.6 88.385 99.81 0.277 0.14 5.1 3.9 20327 19305
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.667 100 0.667 0.667 0.395 0.9 3.9 2923
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 3NTY 2.6 88.38 19305 1006 99.81 0.21338 0.21159 0.2194 0.24724 0.2503 RANDOM 19.05
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] -1.04 -0.66 -0.8 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.116 r_dihedral_angle_4_deg 15.468 r_dihedral_angle_3_deg 13.958 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 3.601 r_long_range_B_other 3.569 r_scangle_other 1.944 r_mcangle_it 1.853 r_mcangle_other 1.853 r_angle_refined_deg 1.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.116 r_dihedral_angle_4_deg 15.468 r_dihedral_angle_3_deg 13.958 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 3.601 r_long_range_B_other 3.569 r_scangle_other 1.944 r_mcangle_it 1.853 r_mcangle_other 1.853 r_angle_refined_deg 1.571 r_scbond_it 1.118 r_scbond_other 1.118 r_mcbond_it 1.069 r_mcbond_other 1.069 r_angle_other_deg 1 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 5092 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction