Crystal structure of GH146 beta-L-arabinofuranosidase Bll3HypBA1 (amino acids 380-1051), ligand-free form
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293.15 | 45% MPD, 0.2 M ammonium acetate, and 0.1 M HEPES-NaOH (pH 7.5) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.13 | 42.38 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 75.231 | α = 90 |
| b = 83.51 | β = 90.66 |
| c = 102.034 | 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 | PIXEL | DECTRIS PILATUS 6M | 2016-11-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.9800 | Photon Factory | BL-17A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.7 | 49.2 | 99.1 | 0.076 | 0.065 | 0.998 | 7.3 | 3.4 | 137533 | 18.21 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.7 | 1.73 | 98.3 | 0.939 | 0.787 | 0.676 | 1 | 3.4 | |||||||||||
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 | 1.7 | 43.57 | 130696 | 6825 | 99.15 | 0.2221 | 0.22018 | 0.23 | 0.25941 | 0.27 | RANDOM | 23.604 | |||||
| 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] | |
| 0.69 | 1.89 | -0.85 | 0.11 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 12.913 |
| r_dihedral_angle_2_deg | 8.509 |
| r_dihedral_angle_1_deg | 6.888 |
| r_long_range_B_refined | 5.034 |
| r_long_range_B_other | 5.019 |
| r_scangle_other | 3.948 |
| r_mcangle_it | 2.714 |
| r_mcangle_other | 2.713 |
| r_scbond_it | 2.528 |
| r_scbond_other | 2.526 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10440 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 650 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |
