5NZE
Complex of S247N mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TI6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 291 | 0.1 M HEPES pH 6.7, 8.5% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.67 | α = 90 |
b = 136.59 | β = 90 |
c = 119.14 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | PIXEL | DECTRIS PILATUS 300K | 2016-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
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 | 1.69 | 49.6 | 93.9 | 0.089 | 0.094 | 0.996 | 11.6 | 4.8 | 101435 | -3 | 22.396 |
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 | 1.69 | 1.73 | 83.2 | 0.712 | 0.7 | 0.821 | 2 | 3.61 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3TI6 | 1.69 | 49.6 | 99406 | 2029 | 93.94 | 0.1876 | 0.1871 | 0.2132 | RANDOM | 16.962 |
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] | |
-0.91 | 1.06 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.807 |
r_dihedral_angle_4_deg | 13.955 |
r_dihedral_angle_3_deg | 12.999 |
r_dihedral_angle_1_deg | 7.455 |
r_angle_refined_deg | 1.802 |
r_angle_other_deg | 1.147 |
r_chiral_restr | 0.119 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5986 |
Nucleic Acid Atoms | |
Solvent Atoms | 795 |
Heterogen Atoms | 207 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |