7RLM
Crystal Structure of Potato Leafroll Virus (PLRV) Coat Protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6SCO | PDB entry 6SCO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 0.1 M Bis-Tris propane, pH 7.7, 26% PEG3350, 0.1 M sodium bromide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.92 | 35.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.863 | α = 79.67 |
b = 67.479 | β = 76.219 |
c = 75.887 | γ = 81.673 |
Symmetry | |
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Space Group | P 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 EIGER2 X 16M | 2018-06-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.979 | APS | 24-ID-C |
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 | 1.504 | 72.86 | 89.13 | 0.072 | 0.997 | 8.6 | 3.3 | 177750 | 20.79 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.504 | 1.558 | 0.315 |
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 | PDB entry 6SCO | 1.8 | 72.86 | 1.15 | 59987 | 3090 | 93.11 | 0.1698 | 0.1672 | 0.2175 | 23.88 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.3672 |
f_angle_d | 0.8862 |
f_chiral_restr | 0.057 |
f_bond_d | 0.0068 |
f_plane_restr | 0.0052 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6542 |
Nucleic Acid Atoms | |
Solvent Atoms | 688 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
PHASER | phasing |
XDS | data reduction |
Aimless | data scaling |