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Comparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M BIS-TRIS (pH 5.5), 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.401 α = 90 b = 101.708 β = 102.547 c = 62.433 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 PIXEL DECTRIS PILATUS3 6M 2023-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.29 58.96 99.96 0.993 11.1 5.8 104403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.36 0.873
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.56 38.51 1.4 104403 1405 99.96 0.1604 0.1601 0.1605 0.1839 0.183 17.16
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.7852 f_angle_d 1.1266 f_chiral_restr 0.0602 f_plane_restr 0.0106 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5193 Nucleic Acid Atoms Solvent Atoms 1016 Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing