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The structure of Human MAT2A in complex with SAM, Adenosine, Methionine and PPNP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P02 PDB ENTRY 2P02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M HEPES PH 7.5, 30 % PEG 600
Crystal Properties Matthews coefficient Solvent content 2 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.972 α = 90 b = 94.074 β = 90 c = 117.216 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 MIRRORS 2014-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.1 73.37 99.1 0.09 24.5 12.3 176512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.14 99 0.09 3.4 9.7
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 PDB ENTRY 2P02 1.09 73.37 144726 7510 99.06 0.10481 0.10384 0.1203 0.12398 0.1371 RANDOM 13.035
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] 1.46 0.12 -1.58
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.162 r_dihedral_angle_2_deg 36.97 r_dihedral_angle_4_deg 18.214 r_sphericity_bonded 12.244 r_dihedral_angle_3_deg 11.93 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 4.369 r_long_range_B_other 2.553 r_rigid_bond_restr 2.308 r_scangle_other 2.096
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.162 r_dihedral_angle_2_deg 36.97 r_dihedral_angle_4_deg 18.214 r_sphericity_bonded 12.244 r_dihedral_angle_3_deg 11.93 r_dihedral_angle_1_deg 6.632 r_long_range_B_refined 4.369 r_long_range_B_other 2.553 r_rigid_bond_restr 2.308 r_scangle_other 2.096 r_angle_refined_deg 1.797 r_scbond_other 1.775 r_scbond_it 1.773 r_mcangle_it 1.145 r_mcangle_other 1.145 r_angle_other_deg 1.035 r_mcbond_it 0.863 r_mcbond_other 0.863 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2963 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing