5KZS
Listeria monocytogenes internalin-like protein lmo2027
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 300 | Protein: 12.6 mg/ml, 0.5 M NaCl, 10 mM Tris pH 8.3, 1 mM TCEP Crystallization condition: Classics II D4 (Qiagen), 0.1 M Citric acid (pH 3.5) and 25% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.95 | 58.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.776 | α = 90 |
b = 157.776 | β = 90 |
c = 36.28 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 300 mm CCD | 2016-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.978 | APS | 21-ID-F |
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 | 2.3 | 30 | 98.6 | 0.09 | 16.6 | 6.2 | 20009 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.34 | 99.6 | 0.571 | 0.881 | 1.9 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
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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 | 5HL3 | 2.3 | 30 | 19031 | 974 | 98.43 | 0.23031 | 0.22784 | 0.27907 | RANDOM | 84.536 |
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] | |
-4.28 | -4.28 | 8.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.09 |
r_dihedral_angle_3_deg | 15.979 |
r_dihedral_angle_4_deg | 14.888 |
r_dihedral_angle_1_deg | 6.57 |
r_long_range_B_refined | 5.028 |
r_long_range_B_other | 5.027 |
r_scangle_other | 2.961 |
r_mcangle_it | 2.847 |
r_mcangle_other | 2.846 |
r_scbond_it | 1.836 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2621 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |