5A19
The structure of MAT2A in complex with PPNP.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2P02 | PDB ENTRY 2P02 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.5 | 0.1 M HEPES PH 7.5, 30 % PEG 600 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2 | 39 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 66.22 | α = 90 |
| b = 95.49 | β = 90 |
| c = 117.7 | 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 2M | MIRRORS | 2014-08-11 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.33 | 74.04 | 99.9 | 0.13 | 20.7 | 13 | 16225 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.34 | 2.4 | 99.9 | 0.6 | 1.7 | 13.7 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2P02 | 2.34 | 57.71 | 15301 | 805 | 99.8 | 0.16549 | 0.16344 | 0.17 | 0.20446 | 0.21 | RANDOM | 28.141 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 0.05 | -0.06 | 0.01 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.62 |
| r_dihedral_angle_4_deg | 21.248 |
| r_dihedral_angle_3_deg | 12.797 |
| r_dihedral_angle_1_deg | 6.406 |
| r_long_range_B_refined | 3.591 |
| r_long_range_B_other | 3.349 |
| r_mcangle_it | 1.726 |
| r_mcangle_other | 1.725 |
| r_scangle_other | 1.674 |
| r_angle_refined_deg | 1.276 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2868 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 145 |
| Heterogen Atoms | 60 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
