4P0D
The T6 backbone pilin of serotype M6 Streptococcus pyogenes has a modular three-domain structure decorated with variable loops and extensions
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 291 | 2.2 M NaKPO4 pH 6.4, 2 % PEG 400, 0.1 M imidazole, 20 mM Imidazole |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.24 | α = 90 |
b = 104.24 | β = 90 |
c = 84.22 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | 110 | CCD | ADSC QUANTUM 210r | 2013-03-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.9 | 24.48 | 89.1 | 0.152 | 0.036 | 16.6 | 18.2 | 36565 | 13.3 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 1.94 | 57.9 | 0.939 | 0.229 | 3.8 | 17.4 | 1592 |
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 | PDB Entry 4K8W | 1.9 | 50 | 36383 | 1834 | 88.62 | 0.2111 | 0.209 | 0.2499 | RANDOM | 22.631 |
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] | |
0.5 | 0.25 | 0.5 | -1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.339 |
r_dihedral_angle_4_deg | 15.819 |
r_dihedral_angle_3_deg | 11.817 |
r_dihedral_angle_1_deg | 6.133 |
r_mcangle_it | 1.831 |
r_angle_refined_deg | 1.256 |
r_mcbond_it | 1.12 |
r_mcbond_other | 1.115 |
r_angle_other_deg | 0.706 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3472 |
Nucleic Acid Atoms | |
Solvent Atoms | 441 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data reduction |
Aimless | data scaling |