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) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5A1I | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| 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 | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.04 | 39.57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.935 | α = 90 |
| b = 93.812 | β = 90 |
| c = 116.773 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.54 | 73.13 | 54501 | 3914 | 98.271 | 0.166 | 0.1624 | 0.18 | 0.2065 | 0.22 | 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 | |
|---|---|
| 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 | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2972 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 392 |
| Heterogen Atoms | 75 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| autoPROC | data scaling |
| MOLREP | phasing |
