6D8W
Crystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin from strain A/Jiangsu/ALSI/2011
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 289 | SEC purified InvbI.18715.a.KN11.PD38282 at 10.18mg/ml (in 25mM MES pH 6.5, 150mM NaCl) was crystallized by sitting drop vapor diffusion at 14C with an equal volume (0.2:0.2uL) of protein:mother liquor (20mM each sodium formate, ammonium acetate, sodium citrate, sodium potassium tartrate, and sodium oxamate, 0.1M HEPES pH6.8, 17.2% PEG 500 MME, 8.6% PEG20k), then directly frozen for data collection. Crystal ID 297353a3 data set sht6-6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.94 | 58.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.3 | α = 110.16 |
b = 113.33 | β = 90.85 |
c = 130.12 | γ = 90.28 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | 2018-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.35 | 43.292 | 97.4 | 0.063 | 0.079 | 0.997 | 11.91 | 2.641 | 146567 | 40.16 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.35 | 2.41 | 96.9 | 0.549 | 0.691 | 0.741 | 2.13 | 2.661 |
Refinement
Statistics | |||||||||||||||||||
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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 | THROUGHOUT | 5vli,2wr0 | 2.35 | 43.292 | 1.98 | 146516 | 2041 | 97.48 | 0.1798 | 0.1792 | 0.2247 | 60.4921 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 21388 |
Nucleic Acid Atoms | |
Solvent Atoms | 916 |
Heterogen Atoms | 121 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |