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Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 292
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M Tris pH 8, 0.2 M LiCl, 10%EG; 19%PEG6000
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.276 α = 90 b = 94.105 β = 90 c = 117.011 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 EIGER X 16M 2023-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979191 SSRF BL10U2
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 1.12 73.33 99.6 0.065 0.071 0.027 0.998 14.8 6.6 143430
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 1.12 1.14 96.1 0.895 1.03 0.492 0.527 4.5
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 8XAR 1.12 58.57 136305 7098 99.52 0.12449 0.12376 0.1238 0.1386 0.1387 RANDOM 12.384
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] -0.38 -0.43 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.717 r_long_range_B_refined 12.826 r_long_range_B_other 12.824 r_dihedral_angle_3_deg 12.583 r_dihedral_angle_1_deg 6.754 r_scangle_other 4.299 r_mcangle_it 2.96 r_mcangle_other 2.96 r_scbond_it 2.773 r_scbond_other 2.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.717 r_long_range_B_refined 12.826 r_long_range_B_other 12.824 r_dihedral_angle_3_deg 12.583 r_dihedral_angle_1_deg 6.754 r_scangle_other 4.299 r_mcangle_it 2.96 r_mcangle_other 2.96 r_scbond_it 2.773 r_scbond_other 2.773 r_mcbond_it 1.915 r_mcbond_other 1.914 r_rigid_bond_restr 1.712 r_angle_refined_deg 1.36 r_angle_other_deg 0.483 r_chiral_restr 0.074 r_gen_planes_refined 0.008 r_bond_refined_d 0.004 r_gen_planes_other 0.002 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 2992 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing