5TRO
1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 295 | Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 178.843 | α = 90 |
b = 72.202 | β = 103.18 |
c = 86.362 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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) | 2016-10-20 | 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) | 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 | 1.8 | 30 | 99.7 | 0.088 | 0.088 | 26.8 | 5.4 | 98204 | -3 | 30.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.83 | 99.3 | 0.749 | 0.793 | 2.3 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.8 | 29.59 | 93238 | 4950 | 99.22 | 0.18088 | 0.17935 | 0.20946 | RANDOM | 43.7 |
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] | |
0.34 | -1.07 | -1.38 | 1.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.828 |
r_dihedral_angle_4_deg | 10.696 |
r_dihedral_angle_3_deg | 10.411 |
r_long_range_B_refined | 5.186 |
r_long_range_B_other | 5.028 |
r_dihedral_angle_1_deg | 3.139 |
r_scangle_other | 1.941 |
r_mcangle_it | 1.739 |
r_mcangle_other | 1.739 |
r_angle_refined_deg | 1.365 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7959 |
Nucleic Acid Atoms | |
Solvent Atoms | 615 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |