4PCG
Structure of Human Polyomavirus 6 (HPyV6) VP1 pentamer
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | 100 mM Tris pH 8.5, 200 mM NaSCN, 13.3% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 183.9 | α = 90 |
b = 89.44 | β = 131.26 |
c = 125.27 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2011-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.00000 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 30 | 99.2 | 14.8 | 4.1 | 140450 | -3 | 28.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.8 | 1.85 | 96.4 | 2.8 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Human Polyomavirus 7 (HPyV7) VP1 pentamer | 1.8 | 30 | 133401 | 7049 | 99.48 | 0.14926 | 0.14794 | 0.17438 | RANDOM | 28.642 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.738 |
r_dihedral_angle_4_deg | 21.117 |
r_dihedral_angle_3_deg | 12.382 |
r_long_range_B_refined | 7.716 |
r_long_range_B_other | 7.676 |
r_dihedral_angle_1_deg | 6.038 |
r_scangle_other | 5.242 |
r_scbond_it | 4.067 |
r_scbond_other | 3.967 |
r_mcangle_other | 2.966 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10042 |
Nucleic Acid Atoms | |
Solvent Atoms | 1070 |
Heterogen Atoms | 46 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XDS | data scaling |
Coot | model building |
PHASER | phasing |