5JUN
PB2 bound to an azaindole inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.7 | 293 | 1 uL protein solution (2.8 mg/mL protein, 50 mM Tris, pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 1 mM anthraquinone-2,6-disulfonic acid disodium salt, 7.5 mM GTP) + 0.4 uL well solution (1.5 M sodium formate, 100 mM sodium citrate, pH 4.7, 10 mM dithiothreitol) suspended over 1 mL of well solution, crystals transferred to a soaking solution (3.25 M sodium formate, 100 mM sodium citrate, pH 4.7) containing 1 mM inhibitor, incubated approximately 15 hours at room temperature, and then transferred to a cryo-preservative solution (soaking solution with 25% v/v glycerol) prior to freezing in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.36 | α = 90 |
b = 81.36 | β = 90 |
c = 54.82 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | CCD | MAR CCD 165 mm | 2011-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 0.979460 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 2.598 | 29.64 | 95.4 | 0.052 | 23.2 | 4.9 | 6190 | 69.46 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.74 | 99.9 | 0.545 | 1.4 | 4.7 |
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 | 4NCE | 2.69 | 29.64 | 5549 | 276 | 95 | 0.176 | 0.176 | 0.189 | RANDOM | 64.59 |
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] | |
-3.8039 | -3.8039 | 7.6077 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 20.27 |
t_omega_torsion | 3.71 |
t_angle_deg | 1.13 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1254 |
Nucleic Acid Atoms | |
Solvent Atoms | 17 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |