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Crystal structure of AKR1C3 complexed with glimepiride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 15-20% (w/v) PEG 8000, 100 mM MES, 0.14M NaCl
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47 α = 74.65 b = 49.265 β = 86.04 c = 83.723 γ = 69.41
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 2014-12-26 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 Sym I (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 2.3 80.709 99.9 0.155 0.171 0.071 9.2 5.7 30098 30098
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 2.3 2.42 100 0.615 0.615 0.283 1.1 5.6 4378
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 4FAM 2.3 80.709 28584 1514 99.93 0.18671 0.1843 0.1922 0.23234 0.2384 RANDOM 26.613
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] -0.04 0.04 -0.02 0.03 0.05 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_4_deg 17.489 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 6.912 r_long_range_B_refined 6.715 r_long_range_B_other 6.694 r_scangle_other 4.046 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 2.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.02 r_dihedral_angle_4_deg 17.489 r_dihedral_angle_3_deg 13.318 r_dihedral_angle_1_deg 6.912 r_long_range_B_refined 6.715 r_long_range_B_other 6.694 r_scangle_other 4.046 r_mcangle_it 3.371 r_mcangle_other 3.371 r_scbond_it 2.473 r_scbond_other 2.473 r_mcbond_it 2.097 r_mcbond_other 2.092 r_angle_refined_deg 1.829 r_angle_other_deg 1.047 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 5048 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction