2WYI
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 | |
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Matthews coefficient | Solvent content |
3.84 | 69 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 178.68 | ¦Á = 90 |
b = 178.68 | ¦Â = 90 |
c = 198.237 | ¦Ã = 90 |
Symmetry | |
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.223 | 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 | |
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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 |