6QWI
Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.64 | 66.23 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 146.096 | α = 90 |
| b = 146.096 | β = 90 |
| c = 140.345 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 4 21 2 |
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 | KB focusing mirrors | 2018-11-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.979260 | ALBA | XALOC |
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 | 2.85 | 48.7 | 76.4 | 0.141 | 0.151 | 0.052 | 0.985 | 10.3 | 7.8 | 27295 | 45.005 | ||||||||
| 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 | 2.85 | 3 | 79.1 | 0.689 | 0.737 | 0.252 | 0.804 | 2.8 | 7.7 | ||||||||||
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 | 1E4I | 2.85 | 48.52 | 25865 | 1405 | 75.55 | 0.18315 | 0.18056 | 0.23128 | RANDOM | 43.586 | ||||||
| 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] | |
| -0.42 | -0.42 | 0.85 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.087 |
| r_dihedral_angle_4_deg | 21.54 |
| r_dihedral_angle_3_deg | 16.423 |
| r_long_range_B_refined | 6.566 |
| r_long_range_B_other | 6.562 |
| r_dihedral_angle_1_deg | 6.426 |
| r_scangle_other | 4.292 |
| r_mcangle_it | 3.911 |
| r_mcangle_other | 3.911 |
| r_scbond_it | 2.622 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7294 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 150 |
| Heterogen Atoms | 50 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
