8P4H

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


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 7.0, 20 % (w/v) PEG 6000, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2845.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.898α = 90
b = 106.742β = 93.18
c = 114.996γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2021-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.7178.399.90.0760.0860.0410.9989.44.3176313
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.7499.90.941.0730.5090.75124.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7178.3167555874799.880.154330.152780.18388RANDOM34.045
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]
0.650.180.68-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.084
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg12.85
r_dihedral_angle_1_deg7.073
r_long_range_B_refined6.971
r_long_range_B_other6.948
r_scangle_other5.221
r_scbond_it3.948
r_scbond_other3.948
r_mcangle_it3.037
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.084
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg12.85
r_dihedral_angle_1_deg7.073
r_long_range_B_refined6.971
r_long_range_B_other6.948
r_scangle_other5.221
r_scbond_it3.948
r_scbond_other3.948
r_mcangle_it3.037
r_mcangle_other3.037
r_mcbond_it2.393
r_mcbond_other2.384
r_angle_refined_deg1.602
r_angle_other_deg1.44
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11771
Nucleic Acid Atoms
Solvent Atoms1075
Heterogen Atoms196

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing