☰ Navigation Tabs
Methyltransferase XisE in complex with SAH, closed state
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 7.5 293 200 mM calcium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.51 α = 80.03 b = 47.56 β = 79.98 c = 85.36 γ = 73.59
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 2024-10-27 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 1.4 50 96 0.057 13 4 132287
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 1.4 1.5 95 0.569 2.9 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 1.4 45.23 125672 6615 95.97 0.16328 0.16232 0.1616 0.18147 0.1803 RANDOM 20.063
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] 0.22 0.19 0.12 -0.84 0.14 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.35 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 11.466 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 2.453 r_long_range_B_other 2.099 r_scangle_other 1.337 r_angle_other_deg 1.24 r_angle_refined_deg 1.172 r_mcangle_it 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.35 r_dihedral_angle_4_deg 17.269 r_dihedral_angle_3_deg 11.466 r_dihedral_angle_1_deg 6.718 r_long_range_B_refined 2.453 r_long_range_B_other 2.099 r_scangle_other 1.337 r_angle_other_deg 1.24 r_angle_refined_deg 1.172 r_mcangle_it 1.135 r_mcangle_other 1.135 r_scbond_it 1.032 r_scbond_other 1.032 r_mcbond_it 0.844 r_mcbond_other 0.843 r_rigid_bond_restr 0.495 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 4408 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing