8P1W

Crystal structure of human methionine adenosyltransferase 2A (MAT2A) in complex with allosteric compound STL232591


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
2.0439.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.132α = 90
b = 93.785β = 90
c = 116.706γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

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
11.1558.9199.40.0570.0530.020.99914.87.1132552
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)
11.151.150.8170.6840.4270.6021.3

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-VALUE1.1558.9091325501024599.4220.1130.11150.129215.494
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]
0.72-0.316-0.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg18.997
r_dihedral_angle_3_deg10.981
r_dihedral_angle_1_deg6.864
r_dihedral_angle_other_3_deg3.38
r_lrange_it2.494
r_lrange_other2.068
r_rigid_bond_restr1.962
r_scangle_it1.683
r_scangle_other1.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg18.997
r_dihedral_angle_3_deg10.981
r_dihedral_angle_1_deg6.864
r_dihedral_angle_other_3_deg3.38
r_lrange_it2.494
r_lrange_other2.068
r_rigid_bond_restr1.962
r_scangle_it1.683
r_scangle_other1.683
r_angle_other_deg1.534
r_angle_refined_deg1.468
r_dihedral_angle_other_6_deg1.457
r_scbond_other1.368
r_scbond_it1.367
r_mcangle_it1.191
r_mcangle_other1.191
r_mcbond_it0.88
r_mcbond_other0.88
r_nbd_refined0.208
r_symmetry_xyhbond_nbd_refined0.193
r_nbd_other0.188
r_symmetry_nbd_other0.182
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.15
r_symmetry_nbd_refined0.116
r_chiral_restr0.086
r_symmetry_nbtor_other0.076
r_bond_other_d0.009
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2963
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing