The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 298 | 11-12% PEG 3350, 0.18-0.205 M ammonium sulfate, and 0.1 M acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.2 | 61.54 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 109.217 | α = 90 |
| b = 91.425 | β = 110.95 |
| c = 152.659 | 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 | CCD | MARMOSAIC 300 mm CCD | M | SINGLE WAVELENGTH | ||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.4 | 44.54 | 0.105 | 2.6 | 100648 | ||||||||||||||
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 | Rigid Body Refinement | THROUGHOUT | 2.4 | 44.54 | 100647 | 5292 | 96.27 | 0.17383 | 0.17072 | 0.171 | 0.23233 | 0.2327 | RANDOM | 24.99 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.125 |
| r_dihedral_angle_4_deg | 21.428 |
| r_dihedral_angle_3_deg | 16.378 |
| r_dihedral_angle_1_deg | 7.141 |
| r_angle_refined_deg | 1.805 |
| r_scangle_it | 0.665 |
| r_mcangle_it | 0.398 |
| r_scbond_it | 0.375 |
| r_mcbond_it | 0.215 |
| r_chiral_restr | 0.12 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15700 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1184 |
| Heterogen Atoms | 280 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SERGUI | data collection |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
