7PA6
JC polyomavirus VP1 in complex with scFv 27C11
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | 100 mM potassium phosphate monohydrate / potassium phosphate dihydrate pH 6.0, 10% (w/v) PEG 8000, 686 mM NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.09 | α = 100.913 |
b = 96.11 | β = 93.012 |
c = 190.41 | γ = 113.835 |
Symmetry | |
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Space Group | P 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 | 93 | PIXEL | DECTRIS PILATUS 2M-F | 2016-04-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.99 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 1.9 | 48.5 | 89.9 | 0.1 | 0.99 | 9.27 | 3.83 | 465782 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 2.01 | 1.19 | 0.5 | 1.15 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3NXG, 4KQ3 | 1.9 | 47.809 | 465782 | 23290 | 97.59 | 0.185 | 0.1835 | 0.2164 | 36.13 |
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] | |
1.146 | 1.239 | -0.33 | -0.626 | -0.557 | -0.758 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.253 |
r_dihedral_angle_4_deg | 15.824 |
r_dihedral_angle_3_deg | 13.666 |
r_lrange_it | 8.463 |
r_lrange_other | 8.452 |
r_dihedral_angle_1_deg | 6.74 |
r_scangle_it | 6.373 |
r_scangle_other | 6.373 |
r_mcangle_it | 4.516 |
r_mcangle_other | 4.516 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 37890 |
Nucleic Acid Atoms | |
Solvent Atoms | 2249 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |