6RFZ
Photorhabdus laumondii lectin PLL2 in complex with D-glucose
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 8% PEG 4000, 150 mM sodium acetate pH 4.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.64 | 53.46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 65.498 | ¦Á = 90 |
b = 71.099 | ¦Â = 103.95 |
c = 86.221 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 1 2 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 PILATUS3 2M | 2018-06-23 | 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 Merge I (Observed) | CC (Half) | 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 | 1.8 | 47.39 | 99 | 0.288 | 0.903 | 3.4 | 3.8 | 35262 | 13.025 |
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 | 1.8 | 1.9 | 98.8 | 1.045 | 0.452 | 1.5 | 3.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.8 | 45.64 | 33419 | 1672 | 98.37 | 0.21156 | 0.21037 | 0.23497 | RANDOM | 15.456 |
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] | |
0.31 | 1.05 | -0.81 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.45 |
r_dihedral_angle_3_deg | 12.008 |
r_dihedral_angle_1_deg | 7.746 |
r_dihedral_angle_4_deg | 7.093 |
r_long_range_B_refined | 3.403 |
r_long_range_B_other | 3.052 |
r_angle_other_deg | 2.388 |
r_angle_refined_deg | 1.192 |
r_mcangle_it | 0.652 |
r_mcangle_other | 0.652 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2616 |
Nucleic Acid Atoms | |
Solvent Atoms | 361 |
Heterogen Atoms | 77 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |