4X7F
Crystal structure of norovirus GII.10 P domain in complex with Nano-25
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3ONU | As search models for molecular replacement PDB code 3ONU was used for GII.10 P domain (molecule 1) and PDB code 3P0G for Nano-25 (molecule 2) |
experimental model | PDB | 3P0G | As search models for molecular replacement PDB code 3ONU was used for GII.10 P domain (molecule 1) and PDB code 3P0G for Nano-25 (molecule 2) |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | PEG3350, ammonium dihydrogen phosphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.28 | α = 90 |
b = 112.98 | β = 90 |
c = 142.89 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-F | 2013-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.984 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.7 | 46.59 | 99.1 | 0.056 | 0.067 | 14.33 | 4.7 | 88133 | -3 | 24.11 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.8 | 96.8 | 0.355 | 0.487 | 2.58 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | As search models for molecular replacement PDB code 3ONU was used for GII.10 P domain (molecule 1) and PDB code 3P0G for Nano-25 (molecule 2) | 1.7 | 46.587 | 1.09 | 88133 | 8313 | 97.44 | 0.1612 | 0.1599 | 0.1868 | 32.6161 |
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 |
f_dihedral_angle_d | 12.468 |
f_angle_d | 1.191 |
f_chiral_restr | 0.06 |
f_bond_d | 0.01 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6330 |
Nucleic Acid Atoms | |
Solvent Atoms | 464 |
Heterogen Atoms | 108 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |
PHASER | phasing |