8DHN
The N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-3-hydroxy-2-(5-methyl-1,2,4-oxadiazol-3-yl)pyridin-4(1H)-one
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6E6V |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.21 | 44.33 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75.034 | α = 90 |
b = 75.034 | β = 90 |
c = 121.24 | 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 | CCD | APEX II CCD | 2021-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.4 | 65.01 | 99.9 | 0.1 | 0.102 | 1 | 20 | 29 | 15004 | 47.41 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.4 | 2.48 | 1.439 | 0.33 | 0.84 | 2 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6E6V | 2.4 | 64.98 | 1.33 | 15004 | 1509 | 99.74 | 0.2062 | 0.2006 | 0.2563 | 54.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.2003 |
f_angle_d | 0.6201 |
f_chiral_restr | 0.0406 |
f_bond_d | 0.0042 |
f_plane_restr | 0.0028 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1466 |
Nucleic Acid Atoms | |
Solvent Atoms | 83 |
Heterogen Atoms | 17 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
APEX 2 | data reduction |
APEX 2 | data scaling |
PHASER | phasing |