4QPB
Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans crystallized in the absence of phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QP5 | pdb entry 4QP5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 6 mM pentapeptide GGSGG, 0.1 M Tris (base), Bicine pH 8.5, 0.1 M amino acids (L-Na-glutamate, alanine (racemic), glycine; lysine-HCl (racemic); serine (racemic)), 30% v/v precipitant (ethylene glycol, PEG 8000)., VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.289 | α = 90 |
b = 107.318 | β = 97.63 |
c = 34.307 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS PILATUS 6M | 2013-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.78 | 35 | 99.1 | 0.167 | 7.52 | 2.74 | 23389 | 23389 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.78 | 1.89 | 98.8 | 0.586 | 2.1 | 2.73 | 3748 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 4QP5 | 1.78 | 33.99 | 23387 | 23387 | 707 | 99.19 | 0.21133 | 0.21025 | 0.24432 | THIN RESOLUTION SHELLS | 12.819 |
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] | |
-1.36 | 0.02 | 1.61 | -0.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.937 |
r_dihedral_angle_4_deg | 22.563 |
r_dihedral_angle_3_deg | 13.202 |
r_dihedral_angle_1_deg | 6.904 |
r_scangle_it | 3.932 |
r_scbond_it | 2.679 |
r_angle_refined_deg | 1.754 |
r_mcangle_it | 1.684 |
r_angle_other_deg | 1.388 |
r_mcbond_it | 1.043 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2082 |
Nucleic Acid Atoms | |
Solvent Atoms | 237 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |