BpGH86A: A beta-porphyranase of glycoside hydrolase family 86 from the human gut bacterium Bacteroides plebeius
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 27% PEG MME 2000, 0.1 M POTASSIUM THIOCYANATE AND 150 MM SODIUM IODIDE | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.8 | 56 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 71.33 | α = 90 |
| b = 87.7 | β = 90 |
| c = 114.45 | 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 | 100 | M | SINGLE WAVELENGTH | |||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-1 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.33 | 31.41 | 99 | 0.06 | 15.8 | 7.3 | 163194 | 2 | |||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | NONE | 1.33 | 69.61 | 154892 | 8189 | 99.66 | 0.13813 | 0.13742 | 0.15 | 0.15157 | 0.16 | RANDOM | 11.553 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
| -0.32 | 0.27 | 0.05 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.769 |
| r_dihedral_angle_4_deg | 15.774 |
| r_dihedral_angle_3_deg | 11.044 |
| r_dihedral_angle_1_deg | 6.31 |
| r_scangle_it | 4.767 |
| r_scbond_it | 3.439 |
| r_mcangle_it | 2.531 |
| r_mcbond_it | 1.644 |
| r_angle_refined_deg | 1.632 |
| r_rigid_bond_restr | 1.421 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4475 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 594 |
| Heterogen Atoms | 107 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
