7BNY
Structure of 2A protein from encephalomyocarditis virus (EMCV)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.7 | 294 | Purified EMCV 2A was concentrated to 5.9 mg/ml in 10 mM HEPES pH 7.9, 1.0 M NaCl, 2.0 mM DTT Drops were prepared by mixing 200 nL protein and 200 nL crystallization buffer: 0.625 M ammonium sulfate, 0.15 M tri-sodium citrate pH 5.7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.56 | α = 90 |
b = 91.56 | β = 90 |
c = 316.39 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 | 2018-06-24 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2018-09-21 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97958 | Diamond | I03 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97635, 0.97965, 0.97974 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.62 | 43.91 | 100 | 0.227 | 0.053 | 0.998 | 11.5 | 18.9 | 24668 | 54.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.62 | 2.67 | 99.8 | 2.766 | 0.64 | 0.728 | 1 | 19.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | FREE R-VALUE | 2.62 | 43.91 | 1.34 | 24568 | 1207 | 99.66 | 0.2267 | 0.2254 | 0.2511 | 75.03 |
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 | 25.6104 |
f_angle_d | 0.7407 |
f_chiral_restr | 0.0465 |
f_plane_restr | 0.0068 |
f_bond_d | 0.0033 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4384 |
Nucleic Acid Atoms | |
Solvent Atoms | 147 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
GDA | data collection |
xia2 | data reduction |
XDS | data reduction |
Aimless | data scaling |
SHARP | phasing |
SHELXD | phasing |
PHENIX | refinement |
ARP/wARP | model building |
Coot | model building |