2WYH
Structure of the Streptococcus pyogenes family GH38 alpha-mannosidase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8.5 | 12 MG/ML PROTEIN WITH 100 MM TRIS, PH 8.5, 1.5 M (NH4)2SO4, 12% V/V GLYCEROL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 92.573 | ¦Á = 90 |
b = 88.502 | ¦Â = 108.97 |
c = 134.688 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 2007-02-02 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 1.9 | 50 | 99.4 | 0.05 | 14.4 | 3.3 | 152396 | 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 | 1.9 | 1.97 | 99.1 | 0.46 | 1.95 | 3 |
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 | NONE | 1.9 | 127 | 152396 | 8041 | 99.1 | 0.179 | 0.177 | 0.205 | RANDOM | 15.96 |
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] | |
-0.48 | -0.48 | -0.25 | 0.43 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.228 |
r_dihedral_angle_4_deg | 13.823 |
r_dihedral_angle_3_deg | 12.96 |
r_dihedral_angle_1_deg | 7.197 |
r_scangle_it | 2.474 |
r_scbond_it | 1.494 |
r_angle_refined_deg | 1.134 |
r_mcangle_it | 0.844 |
r_mcbond_it | 0.44 |
r_chiral_restr | 0.078 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14343 |
Nucleic Acid Atoms | |
Solvent Atoms | 915 |
Heterogen Atoms | 82 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHARP | phasing |
SHELX | phasing |
RESOLVE | phasing |