3K39
Crystal Structure of B/Perth Neuraminidase D197E mutant in complex with Peramivir
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3K38 | PDB ENTRY 3K38 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 281.15 | 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, HANGING DROP, temperature 281.15K, PH7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.964 | α = 90.03 |
b = 124.874 | β = 92.11 |
c = 125.245 | γ = 91.27 |
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 | ADSC QUANTUM 210r | BEAMLINE OPTICS | 2008-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.95665 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 62.58 | 95.2 | 0.209 | 4.7 | 3.4 | 286795 | 286795 | -1 | -1 | 20.47 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.42 | 90.3 | 0.557 | 2 | 2.9 | 39780 |
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 | PDB ENTRY 3K38 | 2.54 | 55.9 | 191318 | 10637 | 90.6 | 0.19884 | 0.19801 | 0.21388 | RANDOM | 22.374 |
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] | |
53.08 | -0.87 | -5.22 | -30.55 | -9.6 | -22.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.438 |
r_dihedral_angle_3_deg | 17.376 |
r_dihedral_angle_4_deg | 14.082 |
r_dihedral_angle_1_deg | 7.061 |
r_scangle_it | 2.42 |
r_angle_refined_deg | 1.569 |
r_scbond_it | 1.539 |
r_mcangle_it | 0.915 |
r_mcbond_it | 0.474 |
r_chiral_restr | 0.102 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 48112 |
Nucleic Acid Atoms | |
Solvent Atoms | 928 |
Heterogen Atoms | 612 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |