8BSA
Vc1313-LBD bound to D-arginine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.7 | 293 | 0.1 M Tris (base) bicine pH 8.6 - 8.8, 17 - 21% v/v PEG 500 MME, 8 - 10% w/v PEG 20000.Before setting up the drops 13 mg ml-1 Vc1313-LBD was mixed with 10 mM D-arginine from a 200 mM stock. The protein-ligand mixture was then mixed with reservoir solution in a 3:1 ratio. Before flash freezing the crystal in liquid nitrogen, the PEG concentrations were raised to 23% v/v PEG 500*MME, 12% w/v PEG 20000. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.499 | α = 75.81 |
b = 44.557 | β = 84.49 |
c = 55.337 | γ = 74.74 |
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 PILATUS3 X 2M | 2021-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.8731 | ESRF | ID23-2 |
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 | 1.9 | 37.12 | 96.32 | 0.0864 | 0.1031 | 0.0554 | 0.994 | 7.46 | 3.4 | 26099 | 35.43 |
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 | 1.9 | 1.968 | 0.58 |
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-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | AB INITIO PHASING | FREE R-VALUE | 1.9 | 37.12 | 1.98 | 26087 | 96.32 | 0.1914 | 0.2245 | 42.95 |
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 | 4.9578 |
f_angle_d | 0.9555 |
f_chiral_restr | 0.0422 |
f_plane_restr | 0.0084 |
f_bond_d | 0.0074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2516 |
Nucleic Acid Atoms | |
Solvent Atoms | 143 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
Arcimboldo | phasing |
PHASER | phasing |
Coot | model building |
XDS | data reduction |
XDS | data scaling |