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Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric compound 2
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 39.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.935 α = 90 b = 93.812 β = 90 c = 116.773 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 1.54 73.13 99.7 0.092 0.085 0.033 0.999 14.4 7.7 55294
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 1.54 1.57 1.247 1.1651 0.437 0.651 1.6
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 1.54 73.13 54501 3914 98.271 0.166 0.1624 0.1765 0.2065 0.2174 18.651
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] 2.913 -0.854 -2.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 51.259 r_dihedral_angle_2_deg 33.68 r_dihedral_angle_other_6_deg 26.01 r_dihedral_angle_6_deg 16.849 r_dihedral_angle_4_deg 16.454 r_dihedral_angle_3_deg 11.293 r_dihedral_angle_1_deg 6.979 r_lrange_it 3.436 r_rigid_bond_restr 3.18 r_lrange_other 2.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 51.259 r_dihedral_angle_2_deg 33.68 r_dihedral_angle_other_6_deg 26.01 r_dihedral_angle_6_deg 16.849 r_dihedral_angle_4_deg 16.454 r_dihedral_angle_3_deg 11.293 r_dihedral_angle_1_deg 6.979 r_lrange_it 3.436 r_rigid_bond_restr 3.18 r_lrange_other 2.695 r_scangle_it 1.91 r_scangle_other 1.91 r_scbond_it 1.632 r_scbond_other 1.632 r_mcangle_it 1.409 r_mcangle_other 1.409 r_angle_other_deg 1.372 r_angle_refined_deg 1.37 r_mcbond_other 1.107 r_mcbond_it 1.105 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.17 r_xyhbond_nbd_refined 0.159 r_nbtor_refined 0.153 r_nbd_other 0.147 r_symmetry_nbd_refined 0.122 r_chiral_restr 0.073 r_symmetry_nbtor_other 0.068 r_symmetry_xyhbond_nbd_other 0.021 r_bond_other_d 0.009 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2972 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling MOLREP phasing