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SAM-dependent C6-FPP methytransferase from Streptomyces varsoviensis in complex with SAH and FPP
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, SITTING DROP 6.5 293 0.1 M MES, 0.2 M MgCl2, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.56 α = 90 b = 133.33 β = 90 c = 231.42 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2025-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.2 30 98.7 0.114 7.5 3.8 201666
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 2.2 2.3 99.6 0.745 2 3.8
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 (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 2.2 30 191520 10080 98.62 0.21027 0.20885 0.2077 0.23737 0.2367 RANDOM 39.649
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] 1.71 0.71 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.567 r_dihedral_angle_3_deg 13.82 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_1_deg 4.967 r_long_range_B_refined 2.131 r_mcangle_it 0.888 r_angle_refined_deg 0.632 r_mcbond_it 0.606 r_scbond_it 0.572 r_rigid_bond_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.567 r_dihedral_angle_3_deg 13.82 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_1_deg 4.967 r_long_range_B_refined 2.131 r_mcangle_it 0.888 r_angle_refined_deg 0.632 r_mcbond_it 0.606 r_scbond_it 0.572 r_rigid_bond_restr 0.169 r_chiral_restr 0.053 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26016 Nucleic Acid Atoms Solvent Atoms 820 Heterogen Atoms 292
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing