6FS9
Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5FML | PDB:5FML |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.71 | 54.56 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 63.71 | ¦Á = 90 |
b = 63.71 | ¦Â = 90 |
c = 125.41 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | I 41 |
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 2M | 2017-10-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 2.28 | 56.8 | 93.5 | 0.044 | 0.999 | 16.1 | 4.4 | 10663 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.28 | 2.34 | 0.561 | 0.899 | 2.37 |
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:5FML | 2.28 | 56.8 | 10147 | 516 | 93.44 | 0.18177 | 0.17911 | 0.23541 | RANDOM | 62.623 |
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] | |
2.55 | 2.55 | -5.1 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.617 |
r_dihedral_angle_4_deg | 22.89 |
r_dihedral_angle_3_deg | 17.695 |
r_long_range_B_refined | 11.299 |
r_long_range_B_other | 11.297 |
r_scangle_other | 9.53 |
r_mcangle_other | 7.343 |
r_mcangle_it | 7.342 |
r_scbond_it | 6.599 |
r_scbond_other | 6.595 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1494 |
Nucleic Acid Atoms | |
Solvent Atoms | 8 |
Heterogen Atoms | 38 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |