4PIK
Crystal Structure of Banana Lectin bound to dimannose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 293.15 | 10-20% PEG 8000, 0.05M Potassium Phosphate | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.4 | 48.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 50.456 | α = 90 |
| b = 94.708 | β = 97.5 |
| c = 63.347 | 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 | CCD | MARMOSAIC 300 mm CCD | mirrors | 2013-07-24 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07820 | APS | 21-ID-D |
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 | 1.7 | 50 | 99.9 | 0.045 | 15.9 | 3.8 | 64911 | 16.38 | |||||||||||
| 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 | 1.7 | 1.73 | 99.3 | 0.175 | 3.6 | 3239 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.7 | 38.31 | 64824 | 3282 | 99.96 | 0.1646 | 0.1633 | 0.187 | RANDOM | 18.4 | |||||||
| 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] | |
| -2.6994 | -0.1036 | 2.2381 | 0.4613 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_omega_torsion | 4.49 |
| t_other_torsion | 2.54 |
| t_angle_deg | 1.1 |
| t_bond_d | 0.01 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4094 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 576 |
| Heterogen Atoms | 153 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data reduction |
| BUSTER-TNT | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
| HKL-2000 | data scaling |
| BUSTER | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
