4X11
JC Polyomavirus genotype 3 VP1 in complex with GD1a oligosaccharide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NXG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.14 | α = 90 |
b = 96.1 | β = 110.18 |
c = 127.95 | γ = 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 | 2013-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.0 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.25 | 30 | 98.8 | 16.1 | 5.3 | 81125 | 24.9 |
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 | 2.25 | 2.31 | 2.5 | 4.7 |
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 | 3NXG | 2.3 | 30 | 71920 | 3823 | 99.69 | 0.16285 | 0.1608 | 0.20148 | RANDOM | 19.879 |
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] | |
-0.13 | -0.53 | 1.99 | -1.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.613 |
r_dihedral_angle_4_deg | 16.325 |
r_dihedral_angle_3_deg | 12.599 |
r_dihedral_angle_1_deg | 6.507 |
r_long_range_B_other | 5.188 |
r_long_range_B_refined | 5.185 |
r_scangle_other | 3.537 |
r_scbond_it | 2.57 |
r_scbond_other | 2.567 |
r_mcangle_other | 1.918 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9855 |
Nucleic Acid Atoms | |
Solvent Atoms | 809 |
Heterogen Atoms | 149 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
XDS | data reduction |
PHASER | phasing |
XSCALE | data scaling |