3R2I
Crystal Structure of Superantigen-like Protein, Exotoxin SACOL0473 from Staphylococcus aureus subsp. aureus COL
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QEJ | PDB entry 2QEJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 295 | protein at 7.3 mg/ml 0.25 NaCl, 0.01 M Tris pH 8.3 screen:Classics II, H1, 0.2M MgCl, 0.1M Tris pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.614 | α = 90 |
b = 62.614 | β = 90 |
c = 129.075 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | Mirrors | 2011-02-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97917 | APS | 21-ID-D |
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 | 2.3 | 56.33 | 99.6 | 0.096 | 26.1 | 6.5 | 12065 | 12065 | -3 | 36.2 |
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) | |||||||||||
2.3 | 2.34 | 94.6 | 0.444 | 2.5 | 3.5 | 565 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2QEJ | 2.3 | 45 | 11358 | 570 | 99.07 | 0.1923 | 0.1923 | 0.18926 | 0.25482 | RANDOM | 26.949 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.082 |
r_dihedral_angle_3_deg | 12.274 |
r_dihedral_angle_4_deg | 11.68 |
r_scangle_it | 5.96 |
r_scbond_it | 3.774 |
r_dihedral_angle_1_deg | 3.04 |
r_mcangle_it | 2.413 |
r_angle_refined_deg | 1.918 |
r_mcbond_it | 1.264 |
r_angle_other_deg | 0.922 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1585 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms |
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 |