6QCX
Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.4 | 277 | Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 15-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.32 | 76.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 200.407 | α = 90 |
| b = 200.407 | β = 90 |
| c = 256.372 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 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 | 2018-05-29 | 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) | 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 | 3.08 | 50 | 75.2 | 0.076 | 0.086 | 0.999 | 14.3 | 4.8 | 83143 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 3.08 | 3.27 | 61 | 0.756 | 0.888 | 0.54 | 1.7 | ||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5MSG | 3.08 | 173.56 | 79129 | 4024 | 75.17 | 0.20358 | 0.20243 | 0.22582 | RANDOM | 114.342 | ||||||
| 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] | |
| 0.33 | 0.16 | 0.33 | -1.05 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.24 |
| r_dihedral_angle_3_deg | 15.769 |
| r_dihedral_angle_4_deg | 15.191 |
| r_dihedral_angle_1_deg | 5.323 |
| r_long_range_B_refined | 2.301 |
| r_long_range_B_other | 2.301 |
| r_angle_refined_deg | 1.141 |
| r_angle_other_deg | 1.071 |
| r_mcangle_it | 0.833 |
| r_mcangle_other | 0.833 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 17483 |
| Nucleic Acid Atoms | 1084 |
| Solvent Atoms | |
| Heterogen Atoms | 15 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| autoPROC | data scaling |
| PHASER | phasing |
