5DGJ
1.0A resolution structure of Norovirus 3CL protease in complex an oxadiazole-based, cell permeable macrocyclic (20-mer) inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UR9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH), 0.05 M BIS-TRIS, 0.05 M ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.94 | 36.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.169 | α = 90 |
b = 41.176 | β = 109.36 |
c = 61.679 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | PIXEL | DECTRIS PILATUS 6M | 2015-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0000 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 34.21 | 99.5 | 0.047 | 0.994 | 12.1 | 3.2 | 82788 | 10.74 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1 | 1.02 | 90.7 | 0.474 | 0.764 | 1.9 | 2.2 | 3723 |
Refinement
Statistics | |||||||||||||||||||
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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 | 3UR9 | 1 | 32.202 | 1.06 | 82775 | 3986 | 99.44 | 0.1432 | 0.1427 | 0.1544 | 17.1397 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.369 |
f_angle_d | 1.033 |
f_chiral_restr | 0.089 |
f_bond_d | 0.007 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1240 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Aimless | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
XDS | data reduction |