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Methyltransferase XisE in complex with SAH, open state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RFR Methyltransferase XisE in complex with SAH, closed state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 200 mM MgSO4, 20% PEG 4000, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.47 α = 80.45 b = 47.59 β = 80.16 c = 85.41 γ = 73.38
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 2024-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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 1.45 50 96 0.045 15.2 4 119221
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 1.45 1.55 95.3 0.589 2.3 4.1
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 1.45 45.25 113260 5961 96.02 0.15109 0.15009 0.1492 0.16998 0.1692 RANDOM 24.115
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] -0.41 -0.04 0.29 -0.15 -0.67 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_4_deg 17.708 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 6.88 r_long_range_B_refined 3.287 r_long_range_B_other 3.1 r_scangle_other 2.468 r_scbond_it 1.915 r_scbond_other 1.914 r_mcangle_other 1.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.018 r_dihedral_angle_4_deg 17.708 r_dihedral_angle_3_deg 11.94 r_dihedral_angle_1_deg 6.88 r_long_range_B_refined 3.287 r_long_range_B_other 3.1 r_scangle_other 2.468 r_scbond_it 1.915 r_scbond_other 1.914 r_mcangle_other 1.847 r_mcangle_it 1.845 r_mcbond_it 1.397 r_mcbond_other 1.397 r_angle_other_deg 1.305 r_angle_refined_deg 1.26 r_rigid_bond_restr 0.818 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4308 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing