Crystal structure of CV39L lectin from Chromobacterium violaceum at 1.8 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 290 | 0.1 M sodium acetate, 25% PEG 4000, 0.2M ammonium sulphate, pH 4.6 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.18 | 43.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 65.709 | α = 90 |
| b = 123.781 | β = 90 |
| c = 180.935 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 2013-10-31 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.967 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.8 | 80.93 | 100 | 0.102 | 0.999 | 14.7 | 7.5 | 137285 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.8 | 1.9 | 100 | 0.363 | 0.953 | 4.9 | 7.5 | ||||||||||||
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 (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.8 | 73.04 | 130295 | 6893 | 99.96 | 0.15458 | 0.15279 | 0.15 | 0.18852 | 0.18 | RANDOM | 12.009 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| 1.64 | -1.67 | 0.03 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.232 |
| r_dihedral_angle_4_deg | 28.84 |
| r_dihedral_angle_3_deg | 11.647 |
| r_dihedral_angle_1_deg | 7.404 |
| r_long_range_B_refined | 4.354 |
| r_long_range_B_other | 4.168 |
| r_scangle_other | 3.132 |
| r_scbond_it | 2.202 |
| r_scbond_other | 2.202 |
| r_angle_refined_deg | 2.014 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10790 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1275 |
| Heterogen Atoms | 100 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| MOLREP | phasing |
