5A0L
N-terminal thioester domain of fibronectin-binding protein SfbI from Streptococcus pyogenes
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1 M ZINC ACETATE, 0.1 M HEPES PH 7.5, 14% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 59.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 165.12 | α = 90 |
b = 165.12 | β = 90 |
c = 42.52 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 PILATUS | 2014-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.35 | 52.22 | 99.9 | 0.05 | 18.7 | 9.2 | 126127 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.35 | 1.39 | 99.1 | 0.75 | 2.7 | 9.1 |
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 | SAD | THROUGHOUT | NONE | 1.35 | 52.22 | 119869 | 6244 | 99.88 | 0.13173 | 0.13069 | 0.15269 | RANDOM | 23.639 |
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] | |
0.17 | 0.17 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 54.712 |
r_dihedral_angle_2_deg | 38.936 |
r_sphericity_bonded | 17.496 |
r_dihedral_angle_4_deg | 16.07 |
r_dihedral_angle_3_deg | 11.067 |
r_dihedral_angle_1_deg | 5.713 |
r_scbond_it | 3.519 |
r_rigid_bond_restr | 3.349 |
r_mcangle_it | 2.986 |
r_mcbond_it | 2.509 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3296 |
Nucleic Acid Atoms | |
Solvent Atoms | 457 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHENIX | phasing |