Neutron structure of GH1 beta-glucosidase Td2F2 ligand-free form at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3WH5 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 293 | Protein solution: protein 20mg/mL, 5mM Tris-DCl (pD 8.9), Reservoir solution: 0.1M CHES (pD 9.5), 0.912M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4 in heavy water |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.37 | 48.08 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 69.72 | α = 90 |
| b = 71.03 | β = 90 |
| c = 97.29 | 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 | 293 | PIXEL | DECTRIS PILATUS 6M | | 2021-10-20 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | DIFFRACTOMETER | iBIX | | 2021-06-29 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | Photon Factory | BL-5A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.28-6.19 | JPARC MLF | BL-03 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.19 | 44.3 | 99.6 | 0.079 | | | 0.033 | 0.998 | | 11.4 | 6.6 | | 154133 | -3 | -3 | |
| 2 | 1.8 | 22.15 | 99.1 | 0.25 | | | 0.093 | 0.983 | | 8.6 | 8 | | 45104 | -3 | -3 | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.19 | 1.21 | | 0.829 | | | 0.347 | 0.755 | | | 6.4 | |
| 2 | 1.8 | 1.86 | | 0.972 | | | 0.41 | 0.466 | | 1.7 | 6.3 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | MOLECULAR REPLACEMENT | 1.19 | 44.3 | | | | 154041 | 7694 | 99.5 | | 0.1532 | 0.1524 | 0.1488 | 0.1676 | 0.173 | Random selection | 22.95 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.8 | 22.15 | | | | 45096 | 2256 | 99.23 | | 0.1504 | 0.1492 | | 0.1732 | | Random selection | |
| 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 |
|---|
| f_dihedral_angle_d | 14.077 |
| f_angle_d | 1.003 |
| f_chiral_restr | 0.082 |
| f_plane_restr | 0.013 |
| f_bond_d | 0.009 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 3458 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 346 |
| Heterogen Atoms | 13 |
