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Substrate-bound Structure of G355T/Q364H mutant of a Ketoreductase from 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 2.36 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.066 α = 72.67 b = 63.627 β = 67.21 c = 71.586 γ = 89.88
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 6M 2016-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9778 SSRF BL18U1
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 1.96 62.48 94.6 0.1 8.6 1.8 63286
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 1.96 1.99 90.6 0.368 2 1.6
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 1.96 50 60085 3200 94.15 0.18214 0.1803 0.189 0.21656 0.2235 RANDOM 31.437
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] 0.87 0.11 -0.55 -0.9 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.095 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.05 r_long_range_B_other 8.213 r_long_range_B_refined 8.21 r_dihedral_angle_1_deg 6.731 r_scangle_other 6.218 r_scbond_it 4.104 r_scbond_other 4.104 r_mcangle_it 3.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.095 r_dihedral_angle_4_deg 17.516 r_dihedral_angle_3_deg 14.05 r_long_range_B_other 8.213 r_long_range_B_refined 8.21 r_dihedral_angle_1_deg 6.731 r_scangle_other 6.218 r_scbond_it 4.104 r_scbond_other 4.104 r_mcangle_it 3.789 r_mcangle_other 3.789 r_mcbond_it 2.791 r_mcbond_other 2.791 r_angle_refined_deg 1.088 r_angle_other_deg 0.58 r_chiral_restr 0.062 r_gen_planes_refined 0.016 r_bond_refined_d 0.007 r_gen_planes_other 0.003 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 6946 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing