8P1T

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with SAM and allosteric inhibitor Z237451470


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A1I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.10 M HEPES pH 8.0, 8 - 12%(v/v) Ethylene glycol, 8 - 10.0% (w/v) PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.0339.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.858α = 90
b = 93.482β = 90
c = 116.793γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.1807CLSI08ID-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4454.981000.0970.090.0340.9914.1867105
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)RedundancyNumber Unique Reflections (All)
11.441.471.6161.5110.5680.6141.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.44254.97667100475599.9820.120.11750.151316.737
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
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg50.756
r_dihedral_angle_2_deg33.799
r_dihedral_angle_4_deg18.641
r_dihedral_angle_3_deg11.283
r_dihedral_angle_6_deg11
r_dihedral_angle_1_deg6.859
r_lrange_it3.078
r_lrange_other2.487
r_rigid_bond_restr1.983
r_scangle_it1.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg50.756
r_dihedral_angle_2_deg33.799
r_dihedral_angle_4_deg18.641
r_dihedral_angle_3_deg11.283
r_dihedral_angle_6_deg11
r_dihedral_angle_1_deg6.859
r_lrange_it3.078
r_lrange_other2.487
r_rigid_bond_restr1.983
r_scangle_it1.88
r_scangle_other1.88
r_scbond_it1.53
r_scbond_other1.529
r_angle_other_deg1.468
r_angle_refined_deg1.404
r_mcangle_it1.391
r_mcangle_other1.391
r_mcbond_it1.103
r_mcbond_other1.103
r_nbd_refined0.21
r_symmetry_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.181
r_nbtor_refined0.161
r_nbd_other0.16
r_symmetry_nbd_refined0.155
r_metal_ion_refined0.143
r_xyhbond_nbd_refined0.125
r_chiral_restr0.079
r_symmetry_nbtor_other0.073
r_symmetry_xyhbond_nbd_other0.065
r_bond_other_d0.009
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2972
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing