6ZIV
Crystal structure of a Beta-glucosidase from Alicyclobacillus acidiphilus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | condition H3 (0.1 M Bis-Tris pH 5.5 and 25% (w/v) PEG3350) from the JCSG screen (Molecular Dimensions) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.654 | α = 91.616 |
b = 91.644 | β = 90.422 |
c = 159.342 | γ = 89.988 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS PILATUS 6M | 2019-10-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 0.9139 | ELETTRA | 11.2C |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.55 | 159.2743 | 91.1 | 0.098 | 0.996 | 9 | 84.9 | 367007 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.55 | 1.64 | 0.561 | 0.608 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | sequence | 1.95 | 46.55 | 247956 | 24694 | 95.977 | 0.266 | 0.2622 | 0.2963 | 11.898 |
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] | |
-0.37 | 0.05 | -0.046 | 0.268 | 0.119 | 0.096 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.117 |
r_dihedral_angle_4_deg | 18.34 |
r_dihedral_angle_3_deg | 13.714 |
r_dihedral_angle_1_deg | 6.268 |
r_lrange_it | 4.389 |
r_scangle_it | 1.414 |
r_mcangle_it | 1.387 |
r_angle_refined_deg | 1.31 |
r_scbond_it | 0.937 |
r_mcbond_it | 0.891 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28359 |
Nucleic Acid Atoms | |
Solvent Atoms | 1952 |
Heterogen Atoms | 189 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
STARANISO | data scaling |
BALBES | phasing |