3KZW
Crystal structure of cytosol aminopeptidase from Staphylococcus aureus COL
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GYT | PDB entry 1gyt |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 70% MPD, 0.1M HEPES, pH 7.5, 0.5M sodium chloride, 0.01M Tris-HCl, pH 8.3, JCSG+, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 143.383 | α = 90 |
b = 154.733 | β = 90 |
c = 340.101 | 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 225 mm CCD | Beryllium lenses | 2008-07-25 | 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 | 2.7 | 44.62 | 98.8 | 0.139 | 0.139 | 9.19 | 4.8 | 207017 | 204154 |
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 1gyt | 2.7 | 44.62 | 207017 | 155647 | 8205 | 79.15 | 0.22234 | 0.22234 | 0.22139 | 0.2402 | RANDOM | 4.572 |
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] | |
0.87 | -0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.524 |
r_dihedral_angle_4_deg | 13.611 |
r_dihedral_angle_3_deg | 13.258 |
r_dihedral_angle_1_deg | 4.668 |
r_angle_refined_deg | 0.841 |
r_scangle_it | 0.31 |
r_mcangle_it | 0.25 |
r_scbond_it | 0.18 |
r_mcbond_it | 0.138 |
r_chiral_restr | 0.057 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 45906 |
Nucleic Acid Atoms | |
Solvent Atoms | 698 |
Heterogen Atoms | 106 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |