3R2T
2.2 Angstrom Resolution Crystal Structure of Superantigen-like Protein from Staphylococcus aureus subsp. aureus NCTC 8325.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KLS | PDB entry 3KLS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | Protein: 7.5mG/mL. 0.5M Sodium chloride, 0.01M Tris, pH 8.3. Screen: Classics II, G5, 0.2M Lithium Sulfate, 0.1M Tris, pH 8.5, 25% (w/v) PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.701 | α = 90 |
b = 72.314 | β = 90 |
c = 123.96 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | Beryllium lenses | 2011-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 2.2 | 30 | 99.9 | 0.076 | 19.6 | 6 | 24026 | 24026 | -3 | 42.1 |
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) | |||||||||||
2.2 | 2.24 | 100 | 0.501 | 3.8 | 6.1 | 1190 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3KLS | 2.21 | 29.63 | 22746 | 22746 | 1229 | 99.58 | 0.20753 | 0.20753 | 0.20518 | 0.2521 | RANDOM | 52.599 |
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] | |
4.15 | -1.28 | -2.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.008 |
r_dihedral_angle_4_deg | 13.492 |
r_dihedral_angle_3_deg | 9.203 |
r_scangle_it | 4.613 |
r_scbond_it | 2.921 |
r_dihedral_angle_1_deg | 2.391 |
r_mcangle_it | 1.877 |
r_angle_refined_deg | 1.569 |
r_mcbond_it | 1.032 |
r_angle_other_deg | 0.821 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3210 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
BALBES | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |