4MBY
Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 293 | 12% (v/v) Isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.53 | α = 90 |
b = 97.21 | β = 96.25 |
c = 234.66 | 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 | 93 | PIXEL | PSI PILATUS 6M | 2011-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
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 | 1.48 | 50 | 98.62 | 17.5 | 3 | 557647 | 549960 | -3 | -3 | 25 |
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 | 1.48 | 1.52 | 98.5 | 2.4 | 3 | 41273 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | LPyV native structure | 1.48 | 48.82 | 557628 | 522360 | 27599 | 98.62 | 0.16634 | 0.16634 | 0.16531 | 0.18578 | RANDOM | 22.628 |
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] | |
-0.04 | -0.62 | 0.47 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.986 |
r_dihedral_angle_4_deg | 17.108 |
r_dihedral_angle_3_deg | 11.133 |
r_long_range_B_refined | 6.892 |
r_dihedral_angle_1_deg | 5.787 |
r_scbond_it | 2.247 |
r_mcangle_it | 1.744 |
r_angle_refined_deg | 1.262 |
r_mcbond_it | 1.119 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20846 |
Nucleic Acid Atoms | |
Solvent Atoms | 2824 |
Heterogen Atoms | 498 |
Software
Software | |
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Software Name | Purpose |
RemDAq | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |