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Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase variant, Abd1-K163R-K311R-F387Y-Y416F, in complex with sinefungin and GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 2 M Ammonium Sulphate, 1.8% Ethylene Glycol, 100 mM Tris-HCl, 10 mM Tris(2-carboxyethl)phosphine hydrochloride
Crystal Properties Matthews coefficient Solvent content 4.47 72.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.779 α = 90 b = 201.17 β = 90 c = 160.532 γ = 90
Symmetry Space Group C 2 2 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 9M 2023-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-1
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 2.73 17.99 99.3 0.194 0.216 0.093 0.983 6.8 5.2 48851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.82 97.3 0.801 0.886 0.375 0.719 5.4
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 FREE R-VALUE 2.8 17.98 43152 2269 99.42 0.17991 0.17806 0.1854 0.21523 0.2179 RANDOM 33.183
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] 0.96 0.63 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.169 r_dihedral_angle_2_deg 9.175 r_long_range_B_refined 8.204 r_long_range_B_other 8.163 r_dihedral_angle_1_deg 6.218 r_scangle_other 5.656 r_mcangle_other 3.93 r_mcangle_it 3.929 r_scbond_it 3.446 r_scbond_other 3.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.169 r_dihedral_angle_2_deg 9.175 r_long_range_B_refined 8.204 r_long_range_B_other 8.163 r_dihedral_angle_1_deg 6.218 r_scangle_other 5.656 r_mcangle_other 3.93 r_mcangle_it 3.929 r_scbond_it 3.446 r_scbond_other 3.407 r_mcbond_it 2.351 r_mcbond_other 2.347 r_angle_refined_deg 1.494 r_angle_other_deg 0.527 r_chiral_restr 0.068 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_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7163 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing