6T3G
3C-like protease from Southampton virus complexed with FMOPL000324a.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6T1Q |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.1 | 294 | 0.2 M ammonium citrate, 12% (v/v) PEG3350. Protein concentration of 5 or 10 mg/ml. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.53 | α = 90 |
b = 88.86 | β = 96.65 |
c = 60.57 | 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 | 2016-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92819 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.63 | 60.16 | 98.5 | 0.054 | 0.064 | 0.035 | 0.998 | 12.5 | 3.3 | 40339 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.63 | 1.67 | 99.3 | 0.716 | 0.878 | 0.501 | 0.534 | 3.1 | 3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 6t1q | 1.63 | 60.16 | 38342 | 1997 | 98.4 | 0.1337 | 0.1301 | 0.2007 | RANDOM | 27.893 |
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] | |
-0.31 | -0.06 | 0.53 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.793 |
r_dihedral_angle_4_deg | 15.519 |
r_dihedral_angle_3_deg | 14.55 |
r_dihedral_angle_1_deg | 7.637 |
r_rigid_bond_restr | 3.341 |
r_angle_refined_deg | 1.714 |
r_angle_other_deg | 1.353 |
r_chiral_restr | 0.087 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2570 |
Nucleic Acid Atoms | |
Solvent Atoms | 261 |
Heterogen Atoms | 55 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
REFMAC | phasing |