6E4C
The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-(2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4AWM | PDB entry 4AWM |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 306 | 30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.19 | 43.81 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.164 | α = 90 |
| b = 75.164 | β = 90 |
| c = 120.628 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 62 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 PILATUS3 6M | 2018-06-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97 | ALS | 5.0.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.35 | 44.28 | 99.9 | 0.034 | 0.035 | 0.01 | 62.6 | 23.3 | 8894 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.35 | 2.44 | 99.6 | 0.456 | 0.475 | 0.13 | 7.5 | 24.1 | |||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 4AWM | 2.35 | 44.28 | 8198 | 672 | 99.72 | 0.20041 | 0.19541 | 0.26027 | RANDOM | 53.646 | ||||||
| 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] | |
| -0.59 | -0.29 | -0.59 | 1.9 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.397 |
| r_dihedral_angle_4_deg | 21.214 |
| r_dihedral_angle_3_deg | 17.195 |
| r_long_range_B_other | 8.388 |
| r_long_range_B_refined | 8.382 |
| r_scangle_other | 7.139 |
| r_dihedral_angle_1_deg | 5.97 |
| r_mcangle_it | 5.195 |
| r_mcangle_other | 5.192 |
| r_scbond_it | 4.894 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1468 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 32 |
| Heterogen Atoms | 30 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
