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Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with allosteric compound STL232591
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 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.132 α = 90 b = 93.785 β = 90 c = 116.706 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 2022-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
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 1.15 58.91 99.4 0.057 0.053 0.02 0.999 14.8 7.1 132552
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 1.15 1.15 0.817 0.684 0.427 0.602 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.15 58.909 132550 10245 99.422 0.113 0.1115 0.1112 0.1292 0.1291 15.494
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] 0.72 -0.316 -0.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 18.997 r_dihedral_angle_3_deg 10.981 r_dihedral_angle_1_deg 6.864 r_dihedral_angle_other_3_deg 3.38 r_lrange_it 2.494 r_lrange_other 2.068 r_rigid_bond_restr 1.962 r_scangle_it 1.683 r_scangle_other 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_4_deg 18.997 r_dihedral_angle_3_deg 10.981 r_dihedral_angle_1_deg 6.864 r_dihedral_angle_other_3_deg 3.38 r_lrange_it 2.494 r_lrange_other 2.068 r_rigid_bond_restr 1.962 r_scangle_it 1.683 r_scangle_other 1.683 r_angle_other_deg 1.534 r_angle_refined_deg 1.468 r_dihedral_angle_other_6_deg 1.457 r_scbond_other 1.368 r_scbond_it 1.367 r_mcangle_it 1.191 r_mcangle_other 1.191 r_mcbond_it 0.88 r_mcbond_other 0.88 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.193 r_nbd_other 0.188 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2963 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing