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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5A1I |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 0.10 M HEPES pH 8.0, 8 - 12%(v/v) Ethylene glycol, 8 - 10.0% (w/v) PEG8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.132 | α = 90 |
b = 93.785 | β = 90 |
c = 116.706 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2022-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 0.9999 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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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) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 1.15 | 58.91 | 99.4 | 0.057 | 0.053 | 0.02 | 0.999 | 14.8 | 7.1 | 132552 |
Highest Resolution Shell | |||||||||||||||||||
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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) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.15 | 1.15 | 0.817 | 0.684 | 0.427 | 0.602 | 1.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.15 | 58.909 | 132550 | 10245 | 99.422 | 0.113 | 0.1115 | 0.1292 | 15.494 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.866 |
r_dihedral_angle_4_deg | 18.997 |
r_dihedral_angle_3_deg | 10.981 |
r_dihedral_angle_1_deg | 6.864 |
r_dihedral_angle_other_3_deg | 3.38 |
r_lrange_it | 2.494 |
r_lrange_other | 2.068 |
r_rigid_bond_restr | 1.962 |
r_scangle_it | 1.683 |
r_scangle_other | 1.683 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2963 |
Nucleic Acid Atoms | |
Solvent Atoms | 406 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
autoPROC | data scaling |
PHASER | phasing |