5C9L
Crystal structure of native PLL lectin from Photorhabdus luminescens at 1.65 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 290 | 0.1 M Tris-HCl, 10% PEG 4000, 0.2 M CaCl2, pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.48 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 71.12 | ¦Á = 90 |
b = 87.677 | ¦Â = 90 |
c = 157.691 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | PSI PILATUS 6M | 2013-08-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.005 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 1.65 | 76.75 | 99.7 | 0.048 | 36.2 | 13.5 | 59360 |
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 | 1.65 | 1.74 | 99.1 | 0.154 | 14.4 | 13.7 |
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 | SAD | THROUGHOUT | 1.65 | 39.15 | 56352 | 3001 | 99.6 | 0.14158 | 0.14063 | 0.15894 | RANDOM | 14.117 |
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] | |
0.28 | 0.07 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.512 |
r_dihedral_angle_4_deg | 15.513 |
r_dihedral_angle_3_deg | 11.615 |
r_dihedral_angle_1_deg | 7.783 |
r_long_range_B_refined | 5.874 |
r_long_range_B_other | 5.563 |
r_scangle_other | 3.882 |
r_scbond_it | 2.821 |
r_scbond_other | 2.812 |
r_mcangle_it | 2.762 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2743 |
Nucleic Acid Atoms | |
Solvent Atoms | 373 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |
SHELXDE | phasing |