4BPZ
Crystal structure of lamA_E269S from Zobellia galactanivorans in complex with a trisaccharide of 1,3-1,4-beta-D-glucan.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4 | 285 | MONO-CRYSTALS OF LAMAE269S IN COMPLEX WITH MLG TRISACCHARIDES WERE OBTAINED AS FOLLOWED: 2 MICROL OF THE MIXTURE ENZYME/OLIGOSACCHARIDES (11,7 MG.ML-1 OF ENZYME, 0,04% (W/V) OF MLG DEGRADATION PRODUCTS) WERE ADDED TO 1 MICROL OF RESERVOIR SOLUTION CONTAINING 100 MM MIB BUFFER PH4.0, 17% OF PEG 1500 AND 10% OF GLYCEROL IN HANGING DROPS AT 12 CELSIUS DEGREE |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.08 | 40.93 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.528 | α = 90 |
| b = 76.485 | β = 90 |
| c = 142.674 | 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 PILATUS 6M | 2011-07-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 | |
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 | 1.13 | 47.56 | 99.2 | 0.07 | 10.5 | 4.9 | 181382 | ||||||||||||
| 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 | 1.13 | 1.19 | 95.7 | 0.66 | 1.9 | 4.2 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4BQ1 | 1.13 | 71.34 | 172173 | 9107 | 99.06 | 0.14404 | 0.14241 | 0.17452 | RANDOM | 20.351 | ||||||
| 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] | |
| 0.86 | -0.86 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.659 |
| r_dihedral_angle_4_deg | 27.662 |
| r_sphericity_free | 27.462 |
| r_sphericity_bonded | 13.422 |
| r_dihedral_angle_3_deg | 12.29 |
| r_rigid_bond_restr | 8.494 |
| r_dihedral_angle_1_deg | 7.678 |
| r_angle_refined_deg | 2.3 |
| r_chiral_restr | 0.235 |
| r_bond_refined_d | 0.026 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4054 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 584 |
| Heterogen Atoms | 70 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
