4RDK
Crystal structure of Norovirus Boxer P domain in complex with Lewis b tetrasaccharide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4RDJ | pdb entry 4RDJ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 290 | 0.1M LiCl, 18%(w/v) PEG 3350, 10%(v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.71 | 54.6 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 139.866 | α = 90 |
b = 139.866 | β = 90 |
c = 64.789 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 |
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 2M-F | mirrors | 2012-06-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-1A | 1.0000 | Photon Factory | BL-1A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.629 | 50 | 100 | 0.079 | 43.2 | 9.9 | 90264 | 90264 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.629 | 1.66 | 100 | 0.503 | 3.6 | 8.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | pdb entry 4RDJ | 1.629 | 31.295 | 1.37 | 90232 | 90232 | 4527 | 99.96 | 0.133 | 0.1312 | 0.1665 | RANDOM | 27.1 |
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] | |
0.0082 | 0.0082 | -0.0164 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.906 |
f_angle_d | 1.054 |
f_chiral_restr | 0.073 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4552 |
Nucleic Acid Atoms | |
Solvent Atoms | 694 |
Heterogen Atoms | 92 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |