6PNV
1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W8B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | Protein: 5.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (G4), 0.2 M Potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.894 | α = 90 |
b = 40.57 | β = 111.61 |
c = 77.994 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 300 mm CCD | C(111) | 2019-06-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.42 | 30 | 96.2 | 0.054 | 0.054 | 0.062 | 0.029 | 22.8 | 4.2 | 67628 | -3 | 13.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.42 | 1.44 | 100 | 0.622 | 0.622 | 0.726 | 0.368 | 0.709 | 2.1 | 3.8 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2w8b | 1.42 | 29.7 | 64124 | 3474 | 95.83 | 0.1635 | 0.1618 | 0.1944 | RANDOM | 16.254 |
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] | |
1.22 | -0.7 | -0.29 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.75 |
r_dihedral_angle_4_deg | 10.771 |
r_dihedral_angle_3_deg | 9.774 |
r_dihedral_angle_1_deg | 4.512 |
r_angle_refined_deg | 1.423 |
r_rigid_bond_restr | 0.983 |
r_angle_other_deg | 0.409 |
r_chiral_restr | 0.065 |
r_gen_planes_refined | 0.053 |
r_gen_planes_other | 0.049 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3101 |
Nucleic Acid Atoms | |
Solvent Atoms | 477 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |