3RZA
Crystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus mu50 at 2.10 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.43 | 293 | 20.0% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M sodium citrate - citric acid pH 5.43, Additive: 0.006 M zinc chloride, 0.006 M calcium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.996 | α = 89.67 |
b = 57.805 | β = 73.38 |
c = 79.857 | γ = 72.36 |
Symmetry | |
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Space Group | P 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 325 mm CCD | double crystal monochromator | 2010-03-12 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.91162,0.97936,0.97911 | SSRL | BL9-2 |
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 | 2.1 | 29.517 | 88.6 | 0.139 | 4.89 | 1.99 | 43307 | -3 | 24.476 |
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 | 2.09 | 2.16 | 73.4 | 0.657 | 1.4 |
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 | MAD | THROUGHOUT | 2.1 | 29.517 | 43307 | 2176 | 96.42 | 0.169 | 0.1668 | 0.2123 | RANDOM | 25.5159 |
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] | |
-0.18 | -0.1 | 0.14 | 0.12 | -0.29 | 0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.985 |
r_dihedral_angle_4_deg | 18.777 |
r_dihedral_angle_3_deg | 13.291 |
r_dihedral_angle_1_deg | 6.876 |
r_scangle_it | 5.322 |
r_scbond_it | 3.508 |
r_mcangle_it | 2.315 |
r_mcbond_it | 1.427 |
r_angle_refined_deg | 1.398 |
r_angle_other_deg | 1.242 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5529 |
Nucleic Acid Atoms | |
Solvent Atoms | 397 |
Heterogen Atoms | 111 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
XSCALE | data scaling |
REFMAC | refinement |
XDS | data reduction |
SHELXD | phasing |