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Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 54
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1M Tris pH 8.0;
0.2M LiCl;
10% EG;
18%-22% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.18 α = 90 b = 94.16 β = 90 c = 117.12 γ = 90
Symmetry Space Group I 2 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 PILATUS3 X 6M 2022-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 1.19 47.12 97.6 0.078 0.081 0.022 0.999 18.2 13.2 117262
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 1.19 1.21 89.3 1.317 1.371 0.379 0.799 12.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7BHR 1.19 47.12 111426 5822 97.39 0.11197 0.11103 0.111 0.12991 0.1299 RANDOM 11.948
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] 3.3 -1.23 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.769 r_long_range_B_refined 12.569 r_long_range_B_other 9.631 r_dihedral_angle_1_deg 6.835 r_dihedral_angle_2_deg 6.438 r_scangle_other 4.399 r_mcangle_other 3.056 r_mcangle_it 3.055 r_scbond_it 2.923 r_scbond_other 2.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.769 r_long_range_B_refined 12.569 r_long_range_B_other 9.631 r_dihedral_angle_1_deg 6.835 r_dihedral_angle_2_deg 6.438 r_scangle_other 4.399 r_mcangle_other 3.056 r_mcangle_it 3.055 r_scbond_it 2.923 r_scbond_other 2.922 r_rigid_bond_restr 2.237 r_mcbond_it 2.013 r_mcbond_other 2.013 r_angle_refined_deg 1.437 r_angle_other_deg 0.499 r_chiral_restr 0.076 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_gen_planes_other 0.003 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2983 Nucleic Acid Atoms Solvent Atoms 534 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction