4KRU
X-ray structure of catalytic domain of endolysin from clostridium perfringens phage phiSM101
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 293 | 20% PEG 3000, 0.2M Lithium sulphate, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.77 | α = 90 |
b = 57.62 | β = 90 |
c = 73.42 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | IMAGE PLATE | RIGAKU RAXIS VII | mirrors (VariMax Optic) | 2012-09-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.37 | 30.96 | 98.4 | 0.024 | 42.5 | 6.15 | 42675 | 42675 | 10.9 |
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 | 1.37 | 1.42 | 85 | 0.071 | 11.7 | 2.52 | 3633 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1JFX | 1.37 | 30.96 | 42613 | 42613 | 2141 | 98.2 | 0.173 | 0.172 | 0.172 | 0.193 | RANDOM | 12.9 |
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] | |
0.81 | -0.35 | -0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.2 |
c_scangle_it | 2.39 |
c_scbond_it | 1.64 |
c_angle_deg | 1.4 |
c_mcangle_it | 1.22 |
c_mcbond_it | 0.82 |
c_improper_angle_d | 0.67 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1710 |
Nucleic Acid Atoms | |
Solvent Atoms | 346 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
MOLREP | phasing |
CNS | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |