Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase complexed with swainsonine
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2WYH | PDB ENTRY 2WYH |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 15 MG/ML 3C CLEAVED SPGH38 MIXED WITH 3% V/V GLYCEROL, 54% V/V TACSIMATE (PH 7.0) AND 2% V/V POLYETHYLENE GLYCOL 6000 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.84 | 69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 178.68 | α = 90 |
| b = 178.68 | β = 90 |
| c = 198.237 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 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 | CCD | ADSC CCD | 2008-11-21 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | ESRF | ID14-1 | |
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 | 2.6 | 50 | 99.8 | 0.05 | 27.7 | 6.8 | 93181 | 2 | |||||||||||
| 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 | 2.6 | 2.69 | 100 | 0.39 | 4.1 | 7 | |||||||||||||
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 Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | PDB ENTRY 2WYH | 2.6 | 132.45 | 93181 | 4888 | 99.7 | 0.189 | 0.187 | 0.19 | 0.223 | RANDOM | 28.09 | |||||
| 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] | |
| 0.89 | 0.89 | -1.77 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.958 |
| r_dihedral_angle_4_deg | 19.023 |
| r_dihedral_angle_3_deg | 14.68 |
| r_dihedral_angle_1_deg | 5.724 |
| r_scangle_it | 2.041 |
| r_scbond_it | 1.193 |
| r_angle_refined_deg | 1.111 |
| r_mcangle_it | 0.782 |
| r_mcbond_it | 0.396 |
| r_chiral_restr | 0.075 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 14274 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 345 |
| Heterogen Atoms | 114 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | model building |
| SCALEPACK | data scaling |
| SHARP | phasing |
| SHELX | phasing |
| RESOLVE | phasing |
| PHASER | phasing |
| REFMAC | refinement |
