3CZ8
Crystal structure of putative sporulation-specific glycosylase ydhD from Bacillus subtilis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | 100mM Sodium cacodylate pH 7.0, 1.2M Sodium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.965 | α = 90 |
b = 84.965 | β = 90 |
c = 188.041 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 77 | CCD | MAR CCD 165 mm | 2008-04-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
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 | 2.15 | 50 | 99.9 | 0.084 | 5.2 | 5.6 | 41723 | -0.5 | 37.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.15 | 2.23 | 99.7 | 0.74 | 1.1 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.2 | 20 | 37618 | 1212 | 99.99 | 0.19787 | 0.19597 | 0.25793 | RANDOM | 49.567 |
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] | |
0.65 | 0.32 | 0.65 | -0.97 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.267 |
r_dihedral_angle_3_deg | 17.194 |
r_dihedral_angle_4_deg | 14.094 |
r_scangle_it | 12.974 |
r_scbond_it | 10.551 |
r_dihedral_angle_1_deg | 9.453 |
r_mcangle_it | 7.339 |
r_mcbond_it | 5.503 |
r_angle_refined_deg | 1.301 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4768 |
Nucleic Acid Atoms | |
Solvent Atoms | 192 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
SHELXD | phasing |
REFMAC | refinement |
MAR345 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |