Structure of the human Langerin carbohydrate recognition domain in complex with mannose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.9 | 293 | Protein: 10mg/ml Langerin in 10 mM Tris/HCl pH 7.5, 5 mM Mannose; Reservoir: 0.1 M Na-cacodylate, 13 %(w/v) PEG4000, 0.1 M MgCl2, 5mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.12 | 41.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 79.71 | α = 90 |
| b = 79.71 | β = 90 |
| c = 89.98 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 42 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2005-11-15 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9796, 0.9798, 0.9080 | BESSY | 14.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.5 | 30 | 99.3 | 0.042 | 18.5 | 4.1 | 89165 | -3 | 24.3 | ||||||||||
| 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) | |||||||||||
| 1.5 | 1.6 | 98.8 | 0.336 | 4 | 4.1 | 15536 | |||||||||||||
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.5 | 30 | 87378 | 1789 | 99.31 | 0.17292 | 0.17221 | 0.17 | 0.20742 | 0.2057 | RANDOM | 22.341 | |||||
| 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] | |
| -0.07 | -0.07 | 0.14 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.086 |
| r_dihedral_angle_3_deg | 12.44 |
| r_dihedral_angle_4_deg | 8.833 |
| r_dihedral_angle_1_deg | 6.863 |
| r_scangle_it | 4.56 |
| r_scbond_it | 3.161 |
| r_mcangle_it | 1.898 |
| r_angle_refined_deg | 1.862 |
| r_mcbond_it | 1.174 |
| r_chiral_restr | 0.132 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4279 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 593 |
| Heterogen Atoms | 52 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345 | data collection |
| SHELXD | phasing |
| SHARP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
