3ZNM
H5 Haemagglutinin in Complex with Sialyl-Lewis X
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IBX | PDB ENTRY 2IBX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 0.1 M HEPES, PH 7.0, 0.05 M MGCL2, 28 - 30 % PEG 550 MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.04 | 70 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 175.56 | ¦Á = 90 |
b = 101.36 | ¦Â = 111.29 |
c = 161.2 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 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 | PIXEL | DECTRIS PILATUS 2M | 2012-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 |
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 | 2.4 | 150.76 | 75.6 | 0.08 | 8.2 | 3.3 | 77719 | 3 | 53.2 |
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 2IBX | 2.4 | 37.15 | 73837 | 3882 | 75.64 | 0.2387 | 0.23777 | 0.25632 | RANDOM | 47.1 |
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] | |
-0.11 | 0.21 | -0.65 | 0.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.912 |
r_dihedral_angle_3_deg | 17.569 |
r_dihedral_angle_4_deg | 16.025 |
r_dihedral_angle_1_deg | 5.225 |
r_angle_refined_deg | 0.997 |
r_angle_other_deg | 0.72 |
r_scbond_it | 0.594 |
r_mcangle_it | 0.287 |
r_mcbond_it | 0.154 |
r_mcbond_other | 0.154 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11595 |
Nucleic Acid Atoms | |
Solvent Atoms | 303 |
Heterogen Atoms | 339 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |