Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin L194P mutant apo form
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4O5N | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 10.5 | 293 | 0.1 M CAPS pH 10.5 and 29% PEG 400 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.33 | 63.11 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 100.491 | α = 90 |
| b = 100.491 | β = 90 |
| c = 383.319 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 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 | 2016-11-29 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0332 | APS | 23-ID-D |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rpim 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 | 2.3 | 50 | 99.6 | 0.1 | 0.03 | 1 | 31.7 | 16.2 | 34068 | 40 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.3 | 2.37 | 95.9 | 0.7 | 0.22 | 0.79 | 1.6 | 9 | |||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4O5N | 2.3 | 50 | 32293 | 1754 | 99.23 | 0.19881 | 0.19691 | 0.2 | 0.2323 | 0.24 | RANDOM | 60.36 | ||||
| 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] | |
| 1.14 | 0.57 | 1.14 | -3.7 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.982 |
| r_dihedral_angle_3_deg | 14.188 |
| r_dihedral_angle_4_deg | 14.084 |
| r_long_range_B_refined | 7.075 |
| r_long_range_B_other | 7.059 |
| r_dihedral_angle_1_deg | 6.405 |
| r_scangle_other | 3.634 |
| r_mcangle_it | 2.292 |
| r_mcangle_other | 2.292 |
| r_scbond_it | 2.087 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3866 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 164 |
| Heterogen Atoms | 184 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data processing |
| HKL-2000 | data scaling |
| PHASER | phasing |
