2J8G
Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a tetrasaccharide- pentapeptide)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1H09 | PDB ENTRY 1H09 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | pH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.52 | α = 90 |
b = 97.39 | β = 90 |
c = 127.14 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2006-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.51 | 63.62 | 92.6 | 0.12 | 3.3 | 5.5 | 58301 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.69 | 1.81 | 71.4 | 0.5 | 1.1 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1H09 | 1.69 | 63.25 | 47556 | 3644 | 92.33 | 0.18656 | 0.18656 | 0.2203 | RANDOM | 20.707 |
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] | |
0.67 | -0.36 | -0.31 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_scangle_it | 3.946 |
c_scbond_it | 2.546 |
c_mcangle_it | 1.888 |
c_angle_deg | 1.496 |
c_mcbond_it | 1.058 |
c_bond_d | 0.016 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2763 |
Nucleic Acid Atoms | |
Solvent Atoms | 454 |
Heterogen Atoms | 72 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |