6F92
Structure of the family GH92 alpha-mannosidase BT3965 from Bacteroides thetaiotaomicron in complex with Mannoimidazole (ManI)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WVY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292 | 20% w/v PEG 3350, 0.2 M NaNO3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.28 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 82.507 | ¦Á = 90 |
b = 186.904 | ¦Â = 91.74 |
c = 95.05 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M | 2014-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.92 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 46.73 | 96.1 | 0.155 | 0.203 | 0.129 | 0.989 | 7.1 | 4.4 | 216402 | 14.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.9 | 1.93 | 96.4 | 0.941 | 1.229 | 0.785 | 0.506 | 1.4 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2WVY | 1.9 | 46.73 | 205642 | 10713 | 96 | 0.17829 | 0.17674 | 0.20766 | RANDOM | 23.019 |
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] | |
2.02 | -0.37 | -1.35 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.181 |
r_dihedral_angle_4_deg | 14.772 |
r_dihedral_angle_3_deg | 13.321 |
r_dihedral_angle_1_deg | 6.826 |
r_long_range_B_refined | 4.344 |
r_long_range_B_other | 4.344 |
r_scangle_other | 2.537 |
r_mcangle_it | 2.171 |
r_mcangle_other | 2.171 |
r_scbond_it | 1.619 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 24089 |
Nucleic Acid Atoms | |
Solvent Atoms | 2305 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |