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) | |||
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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 | 39.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.935 | α = 90 |
b = 93.812 | β = 90 |
c = 116.773 | 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 PILATUS 6M | 2022-01-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 1.1807 | CLSI | 08ID-1 |
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 | 1.54 | 73.13 | 99.7 | 0.092 | 0.085 | 0.033 | 0.999 | 14.4 | 7.7 | 55294 |
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 | 1.54 | 1.57 | 1.247 | 1.1651 | 0.437 | 0.651 | 1.6 |
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 | 1.54 | 73.13 | 54501 | 3914 | 98.271 | 0.166 | 0.1624 | 0.2065 | 18.651 |
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 | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_other_3_deg | 51.259 |
r_dihedral_angle_2_deg | 33.68 |
r_dihedral_angle_other_6_deg | 26.01 |
r_dihedral_angle_6_deg | 16.849 |
r_dihedral_angle_4_deg | 16.454 |
r_dihedral_angle_3_deg | 11.293 |
r_dihedral_angle_1_deg | 6.979 |
r_lrange_it | 3.436 |
r_rigid_bond_restr | 3.18 |
r_lrange_other | 2.695 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2972 |
Nucleic Acid Atoms | |
Solvent Atoms | 392 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
autoPROC | data scaling |
MOLREP | phasing |