4UTF
Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 6.6 | 2.8 M SODIUM ACETATE, PH 6.6 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.2 | 44.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 108.469 | ¦Á = 90 |
| b = 108.469 | ¦Â = 90 |
| c = 67.755 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | I 4 |
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 | 2013-10-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
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 | 1.3 | 39.4 | 100 | 0.04 | 18.8 | 6.6 | 96371 | -3.7 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.3 | 1.32 | 100 | 0.93 | 1.8 | 6.5 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PREVIOUSLY SOLVED NATIVE APO STRUCTURE | 1.3 | 76.7 | 91564 | 4797 | 99.96 | 0.11333 | 0.11196 | 0.13901 | RANDOM | 19.787 | ||||||
| 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] | |
| 0.14 | 0.14 | -0.27 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 37.562 |
| r_dihedral_angle_2_deg | 36.055 |
| r_dihedral_angle_4_deg | 15.771 |
| r_dihedral_angle_3_deg | 13.299 |
| r_sphericity_bonded | 9.582 |
| r_dihedral_angle_1_deg | 6.303 |
| r_mcangle_it | 2.7 |
| r_scangle_it | 2.656 |
| r_rigid_bond_restr | 2.423 |
| r_scbond_it | 2.375 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2815 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 497 |
| Heterogen Atoms | 52 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
