8P1V

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


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
2.0439.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.935α = 90
b = 93.812β = 90
c = 116.773γ = 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
11.5473.1399.70.0920.0850.0330.99914.47.755294
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)
11.541.571.2471.16510.4370.6511.6

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-VALUE1.5473.1354501391498.2710.1660.16240.206518.651
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
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg51.259
r_dihedral_angle_2_deg33.68
r_dihedral_angle_other_6_deg26.01
r_dihedral_angle_6_deg16.849
r_dihedral_angle_4_deg16.454
r_dihedral_angle_3_deg11.293
r_dihedral_angle_1_deg6.979
r_lrange_it3.436
r_rigid_bond_restr3.18
r_lrange_other2.695
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_other_3_deg51.259
r_dihedral_angle_2_deg33.68
r_dihedral_angle_other_6_deg26.01
r_dihedral_angle_6_deg16.849
r_dihedral_angle_4_deg16.454
r_dihedral_angle_3_deg11.293
r_dihedral_angle_1_deg6.979
r_lrange_it3.436
r_rigid_bond_restr3.18
r_lrange_other2.695
r_scangle_it1.91
r_scangle_other1.91
r_scbond_it1.632
r_scbond_other1.632
r_mcangle_it1.409
r_mcangle_other1.409
r_angle_other_deg1.372
r_angle_refined_deg1.37
r_mcbond_other1.107
r_mcbond_it1.105
r_nbd_refined0.189
r_symmetry_xyhbond_nbd_refined0.187
r_symmetry_nbd_other0.17
r_xyhbond_nbd_refined0.159
r_nbtor_refined0.153
r_nbd_other0.147
r_symmetry_nbd_refined0.122
r_chiral_restr0.073
r_symmetry_nbtor_other0.068
r_symmetry_xyhbond_nbd_other0.021
r_bond_other_d0.009
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2972
Nucleic Acid Atoms
Solvent Atoms392
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing