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Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Z237451470
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.10 M HEPES pH 8.0, 8 - 12%(v/v) Ethylene glycol, 8 - 10.0% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.03 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.858 α = 90 b = 93.482 β = 90 c = 116.793 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 PILATUS 6M 2022-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.1807 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.44 54.98 100 0.097 0.09 0.034 0.99 14.1 8 67105
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.47 1.616 1.511 0.568 0.614 1.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.442 54.976 67100 4755 99.982 0.12 0.1175 0.1513 0.1488 16.737
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] 1.141 -0.342 -0.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 50.756 r_dihedral_angle_2_deg 33.799 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 11.283 r_dihedral_angle_6_deg 11 r_dihedral_angle_1_deg 6.859 r_lrange_it 3.078 r_lrange_other 2.487 r_rigid_bond_restr 1.983 r_scangle_it 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 50.756 r_dihedral_angle_2_deg 33.799 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 11.283 r_dihedral_angle_6_deg 11 r_dihedral_angle_1_deg 6.859 r_lrange_it 3.078 r_lrange_other 2.487 r_rigid_bond_restr 1.983 r_scangle_it 1.88 r_scangle_other 1.88 r_scbond_it 1.53 r_scbond_other 1.529 r_angle_other_deg 1.468 r_angle_refined_deg 1.404 r_mcangle_it 1.391 r_mcangle_other 1.391 r_mcbond_it 1.103 r_mcbond_other 1.103 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.161 r_nbd_other 0.16 r_symmetry_nbd_refined 0.155 r_metal_ion_refined 0.143 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.065 r_bond_other_d 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2972 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing