Crystal structure of GH97 glucodextranase mutant E509Q from Flavobacterium johnsoniae in complex with panose
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2D73 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 293 | 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.42 | 49.22 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 290.693 | α = 90 |
| b = 102.708 | β = 90 |
| c = 104.529 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 PILATUS 2M | 2022-06-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | Photon Factory | BL-5A |
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 | 2.34 | 49.23 | 100 | 0.21 | 0.227 | 0.086 | 0.997 | 11.7 | 13.2 | 132638 | |||||||||
| 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 | 2.34 | 2.38 | 100 | 1.347 | 1.453 | 0.542 | 0.734 | 2.1 | 13.8 | ||||||||||
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.34 | 49.23 | 125898 | 6575 | 99.92 | 0.21057 | 0.20827 | 0.21 | 0.25445 | 0.26 | RANDOM | 34.213 | |||||
| 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] | |
| 0.54 | 0.78 | -1.32 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_3_deg | 14.064 |
| r_dihedral_angle_2_deg | 10.44 |
| r_dihedral_angle_1_deg | 7.822 |
| r_long_range_B_refined | 5.658 |
| r_long_range_B_other | 5.654 |
| r_scangle_other | 4.64 |
| r_mcangle_it | 3.875 |
| r_mcangle_other | 3.875 |
| r_scbond_it | 3.203 |
| r_scbond_other | 3.203 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 21902 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 432 |
| Heterogen Atoms | 167 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
