6GHV
Structure of a DC-SIGN CRD in complex with high affinity glycomimetic.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 20% PEG 3350, 200mM Mg(NO3)2, 100mM MES pH6. Protein sample: 150mM NaCl, 4mM CaCl2, 25mM Tris pH8, 2% DMSO, 3.25 mM ligand and 5.54mg/mL protein. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.15 | 60.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.612 | α = 90 |
b = 57.507 | β = 118.67 |
c = 107.247 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 2018-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.1 | 40 | 98.4 | 0.099 | 0.12 | 0.993 | 8.47 | 3.087 | 65455 | 34.771 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.1 | 2.2 | 97.9 | 0.545 | 0.668 | 0.769 | 2.01 | 2.807 |
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 | 1K9I | 2.1 | 40 | 62185 | 3261 | 98.55 | 0.17879 | 0.17592 | 0.23357 | RANDOM | 33.681 |
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] | |
1.48 | 0.55 | -2.31 | 0.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.877 |
r_dihedral_angle_4_deg | 21.049 |
r_dihedral_angle_3_deg | 13.447 |
r_dihedral_angle_1_deg | 6.758 |
r_long_range_B_refined | 6.114 |
r_long_range_B_other | 6.059 |
r_scangle_other | 4.379 |
r_mcangle_it | 3.727 |
r_mcangle_other | 3.727 |
r_scbond_it | 2.901 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6444 |
Nucleic Acid Atoms | |
Solvent Atoms | 660 |
Heterogen Atoms | 344 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |