6FHH
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5M3H |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the thiophospho-serine-5 22-mer Pol II CTD peptide mimic in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.09 | 60.2 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 267.77 | ¦Á = 90 |
b = 147.81 | ¦Â = 97.08 |
c = 88.41 | ¦Ã = 90 |
Symmetry | |
---|---|
Space Group | C 1 2 1 |
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-F | 2017-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.97242 | 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 | 2.7 | 50 | 98.6 | 0.049 | 0.996 | 14.34 | 2.92 | 92066 |
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 | 2.7 | 2.77 | 96.7 | 0.5 | 0.761 | 1.87 | 2.69 |
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 | 5m3h | 2.7 | 50 | 87532 | 4534 | 98.6 | 0.21514 | 0.2129 | 0.25763 | RANDOM | 90.198 |
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] | |
3.28 | 3.39 | -3.86 | -0.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.505 |
r_dihedral_angle_3_deg | 14.455 |
r_dihedral_angle_4_deg | 12.669 |
r_long_range_B_refined | 7.864 |
r_long_range_B_other | 7.861 |
r_dihedral_angle_1_deg | 5.741 |
r_mcangle_it | 4.887 |
r_mcangle_other | 4.887 |
r_scangle_other | 4.758 |
r_mcbond_it | 2.923 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 17644 |
Nucleic Acid Atoms | 600 |
Solvent Atoms | 137 |
Heterogen Atoms | 76 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |