8OFV
Human adenovirus type 53 fiber-knob protein complexed with sialic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 291 | 0.1 M PCTP buffer, 25 % w/v PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.65 | 53.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.555 | α = 90 |
b = 60.406 | β = 99.88 |
c = 243.686 | γ = 90 |
Symmetry | |
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Space Group | P 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 EIGER X 16M | 2019-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91188 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.77 | 92.17 | 98.7 | 0.168 | 0.195 | 0.097 | 0.685 | 6 | 3.8 | 258349 | 17.4 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.77 | 1.8 | 97.7 | 1.707 | 1.967 | 0.966 | 0.327 | 0.6 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.77 | 92.17 | 245379 | 12949 | 98.67 | 0.20937 | 0.20838 | 0.22826 | RANDOM | 27.311 |
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] | |
0.3 | -0.7 | 0.62 | -0.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.565 |
r_dihedral_angle_4_deg | 17.865 |
r_dihedral_angle_3_deg | 15.65 |
r_dihedral_angle_1_deg | 7.946 |
r_long_range_B_refined | 7.067 |
r_long_range_B_other | 7.018 |
r_angle_refined_deg | 1.537 |
r_angle_other_deg | 1.321 |
r_mcangle_it | 1.268 |
r_mcangle_other | 1.268 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17596 |
Nucleic Acid Atoms | |
Solvent Atoms | 1542 |
Heterogen Atoms | 333 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data scaling |
xia2 | data reduction |
PHASER | phasing |