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Crystal structure of O-adenosylmethionine-dependent methyltransferase McbD in complex with SAH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296.15 5 mM SAH under conditions of 0.1 M Tris (pH 8.0), 0.2 M (NH4)2SO4 and 17.2% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.1 60.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.072 α = 90 b = 132.072 β = 90 c = 250.433 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER2 S 9M 2024-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.987 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 39.91 100 0.037 0.052 0.037 0.999 12.6 1.8 26603
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 3 3.18 100 0.809 2.9 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 39.91 26602 1330 99.91 0.2 0.1965 0.1963 0.2715 0.2714 74.322
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] 0.904 0.452 0.904 -2.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.262 r_dihedral_angle_6_deg 14.121 r_dihedral_angle_2_deg 12.992 r_lrange_it 12.982 r_lrange_other 12.981 r_scangle_it 9.887 r_scangle_other 9.886 r_mcangle_other 7.972 r_mcangle_it 7.971 r_dihedral_angle_1_deg 6.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.262 r_dihedral_angle_6_deg 14.121 r_dihedral_angle_2_deg 12.992 r_lrange_it 12.982 r_lrange_other 12.981 r_scangle_it 9.887 r_scangle_other 9.886 r_mcangle_other 7.972 r_mcangle_it 7.971 r_dihedral_angle_1_deg 6.496 r_scbond_it 6.155 r_scbond_other 6.155 r_mcbond_it 5.109 r_mcbond_other 5.108 r_angle_refined_deg 1.445 r_angle_other_deg 0.472 r_symmetry_xyhbond_nbd_refined 0.4 r_symmetry_nbd_refined 0.386 r_nbd_other 0.254 r_nbd_refined 0.234 r_symmetry_nbd_other 0.228 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.182 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.079 r_xyhbond_nbd_other 0.076 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d r_dihedral_angle_other_2_deg
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7014 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling