Structure of a fucose lectin from Kordia zhangzhouensis in complex with methyl-fucoside
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 292 | Morpheus 1 box 1 solution 40 for Mefuc complex or 35% PEG smear medium 10% isopropanol for complex with selenofucoside |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.94 | 58.1 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 87.102 | α = 90 |
| b = 90.522 | β = 90 |
| c = 143.777 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 2 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2018-04-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.97857 | SOLEIL | PROXIMA 1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.55 | 39.25 | 99.8 | 0.041 | 0.051 | 0.031 | 0.999 | 16.9 | 5 | 165158 | 2 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.55 | 1.57 | 98 | 0.654 | 0.824 | 0.496 | 0.773 | 5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | SAD model | 1.55 | 39.25 | 156839 | 8260 | 99.72 | 0.15659 | 0.15536 | 0.17 | 0.18002 | 0.19 | RANDOM | 21.131 | ||||
| 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] | |
| -0.78 | -0.5 | 1.28 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.365 |
| r_dihedral_angle_3_deg | 11.379 |
| r_dihedral_angle_4_deg | 7.667 |
| r_dihedral_angle_1_deg | 6.592 |
| r_long_range_B_refined | 5.122 |
| r_long_range_B_other | 5.121 |
| r_scangle_other | 3.716 |
| r_scbond_it | 2.656 |
| r_scbond_other | 2.656 |
| r_mcangle_it | 2.48 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6824 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1287 |
| Heterogen Atoms | 309 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| SHELXD | phasing |
