6QU8
Adenovirus Serotype 26 (Ad26) in complex with sialic acid, pH8.0
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6FJN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 291 | 0.1 M MIB, 25 % w/v PEG 1500, pH8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.08 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.92 | α = 90 |
b = 85.92 | β = 90 |
c = 85.92 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 6M | 2018-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.91587 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.19 | 42.96 | 100 | 0.085 | 0.088 | 20.7 | 21.4 | 67799 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.19 | 1.22 |
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 | 6FJN | 1.19 | 42.96 | 64286 | 3441 | 100 | 0.14322 | 0.14176 | 0.17201 | RANDOM | 29.632 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.468 |
r_long_range_B_other | 34.402 |
r_long_range_B_refined | 34.099 |
r_mcbond_other | 33.582 |
r_mcbond_it | 33.555 |
r_mcangle_it | 30.079 |
r_mcangle_other | 30.066 |
r_dihedral_angle_4_deg | 22.828 |
r_scangle_other | 21.025 |
r_scbond_it | 18.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1469 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |