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Substrate-bound Structure of a Ketoreductase from the Second Module of the amphotericin Polyketide Synthases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 3.4 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.319 α = 73.09 b = 63.564 β = 67.2 c = 71.886 γ = 89.76
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
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 1.8 50 91.17 0.065 9.8 1.9 76537
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 1.8 1.83 89.5 0.265 2 1.8
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 3MJE 1.8 50 76537 4164 91.17 0.18207 0.1802 0.1904 0.21726 0.2263 RANDOM 23.71
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] 1.15 0.6 -0.08 -0.97 -0.59 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 6.989 r_long_range_B_other 6.35 r_long_range_B_refined 6.347 r_scangle_other 5.118 r_scbond_it 3.502 r_scbond_other 3.501 r_mcangle_it 3.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.043 r_dihedral_angle_4_deg 18.546 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 6.989 r_long_range_B_other 6.35 r_long_range_B_refined 6.347 r_scangle_other 5.118 r_scbond_it 3.502 r_scbond_other 3.501 r_mcangle_it 3.085 r_mcangle_other 3.085 r_mcbond_it 2.26 r_mcbond_other 2.258 r_angle_refined_deg 0.943 r_angle_other_deg 0.556 r_chiral_restr 0.058 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 6938 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing