6RGR
Photorhabdus asymbiotica lectin PHL in complex with L-rhamnose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5MXE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 3.8 M NaCl, 100 mM Hepes, pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.92 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 80.499 | ¦Á = 90 |
b = 80.499 | ¦Â = 90 |
c = 113.413 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 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 | CCD | MARMOSAIC 300 mm CCD | 2016-08-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.3 | 0.8943 | BESSY | 14.3 |
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 | 1.89 | 43.99 | 99.8 | 0.113 | 0.999 | 16.1 | 12.2 | 34618 | 25.4 |
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 | 1.89 | 1.99 | 98.6 | 1.317 | 0.742 | 2 | 12.1 |
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 | 5MXE | 1.89 | 43.99 | 32866 | 1712 | 99.77 | 0.20113 | 0.19967 | 0.22876 | RANDOM | 30.646 |
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] | |
0.7 | 0.35 | 0.7 | -2.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.333 |
r_dihedral_angle_3_deg | 11.546 |
r_dihedral_angle_4_deg | 9.211 |
r_dihedral_angle_1_deg | 8.619 |
r_long_range_B_refined | 4.166 |
r_long_range_B_other | 4.087 |
r_scangle_other | 2.639 |
r_mcangle_it | 2.581 |
r_mcangle_other | 2.58 |
r_mcbond_it | 1.742 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2633 |
Nucleic Acid Atoms | |
Solvent Atoms | 172 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |