7QE3
Se-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 292 | 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA (Arg, Thr, Lys, His), 45 % precipitant mix 6 Morpheus II-2 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3 | 59.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.99 | α = 90 |
| b = 58.579 | β = 90.682 |
| c = 166.424 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 EIGER X 16M | 2020-10-03 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.9788 | SOLEIL | PROXIMA 2 |
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 | 2.2 | 39.775 | 99.5 | 0.095 | 0.12 | 0.072 | 0.996 | 11.2 | 4.9 | 44177 | |||||||||
| 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 | 2.2 | 2.27 | 98.3 | 0.503 | 0.634 | 0.383 | 0.852 | 3 | 5 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | MAD | FREE R-VALUE | 2.2 | 39.775 | 44117 | 2095 | 99.403 | 0.185 | 0.1824 | 0.2312 | 31.486 | ||||||||
| 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] | |
| 0.042 | 1.775 | -1.792 | 1.708 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.464 |
| r_dihedral_angle_4_deg | 16.772 |
| r_dihedral_angle_3_deg | 16.667 |
| r_lrange_it | 8.53 |
| r_lrange_other | 8.525 |
| r_dihedral_angle_1_deg | 7.891 |
| r_scangle_it | 6.803 |
| r_scangle_other | 6.802 |
| r_mcangle_it | 5.201 |
| r_mcangle_other | 5.201 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4983 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 450 |
| Heterogen Atoms | 71 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| XDS | data reduction |
| SHELX | model building |
| SHELX | phasing |
| CRANK2 | phasing |
| BUCCANEER | model building |
