3K38
Crystal Structure of B/Perth Neuraminidase D197E mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3K36 | PDB ENTRY 3K36 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 281.15 | 12-17% w/v PEG 3350, 0.2-0.3M Na2 SO4, 5mM YCl3, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K, PH7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.155 | α = 90.04 |
b = 123.683 | β = 90.19 |
c = 123.789 | γ = 90.19 |
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 | 2008-05-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.95364 | 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 | 2.19 | 61.78 | 94.6 | 0.102 | 8.1 | 2 | 316772 | 316772 | -1 | -1 |
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) | |||||||||||
2.2 | 2.32 | 92.7 | 0.365 | 2.6 | 1.8 | 45355 |
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 3K36 | 2.19 | 61.78 | 300686 | 16084 | 93.25 | 0.19247 | 0.19101 | 0.21989 | RANDOM | 13.721 |
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] | |
39.01 | -2.04 | 6.79 | -17.59 | -2.21 | -21.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.392 |
r_dihedral_angle_3_deg | 16.277 |
r_dihedral_angle_4_deg | 13.47 |
r_dihedral_angle_1_deg | 7.098 |
r_scangle_it | 2.163 |
r_scbond_it | 1.698 |
r_angle_refined_deg | 1.506 |
r_mcangle_it | 0.882 |
r_mcbond_it | 0.585 |
r_chiral_restr | 0.103 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 48112 |
Nucleic Acid Atoms | |
Solvent Atoms | 1304 |
Heterogen Atoms | 340 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |