3PSQ
Crystal structure of Spy0129, a Streptococcus pyogenes class B sortase involved in pilus biogenesis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 291 | 10% PEG 3350, 0.2M zinc acetate, 0.1M sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
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 = 94.511 | α = 90 |
b = 94.511 | β = 90 |
c = 253.519 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 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 | 200 | CCD | ADSC QUANTUM 315r | mirrors | 2006-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.97977 | SSRL | BL9-1 |
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 | 2.32 | 50 | 99.8 | 0.065 | 10 | 25405 | 25357 | -3 | -3 |
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) | |||||||||||
1 | 2.32 | 2.4 | 100 | 0.674 | 4 | 10.2 | 2472 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 2.32 | 30 | 1.5 | 25357 | 23960 | 1262 | 99.5 | 0.238 | 0.20683 | 0.20399 | 0.26248 | RANDOM | 51.401 |
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] | |
0.91 | 0.91 | -1.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.681 |
r_dihedral_angle_4_deg | 18.514 |
r_dihedral_angle_3_deg | 14.225 |
r_dihedral_angle_1_deg | 6.97 |
r_scangle_it | 4.029 |
r_scbond_it | 2.489 |
r_mcangle_it | 1.71 |
r_angle_refined_deg | 1.523 |
r_mcbond_it | 0.914 |
r_chiral_restr | 0.113 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2987 |
Nucleic Acid Atoms | |
Solvent Atoms | 184 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SHARP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |