3RXZ
Crystal structure of putative polysaccharide deacetylase from Mycobacterium smegmatis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | 0.2 M NaCl, 0.1 M imidazole/HCl, 30% PEG8K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.212 | α = 90 |
b = 59.592 | β = 95.35 |
c = 130.387 | γ = 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 | CCD | ADSC QUANTUM 210r | mirrors | 2011-02-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97903 | APS | 19-BM |
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 | 2.01 | 50 | 99.6 | 0.103 | 15.7 | 3.3 | 81570 | 81277 | -3 | 31.34 |
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 | 2.01 | 2.05 | 99.4 | 0.648 | 2 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.01 | 29.13 | 81256 | 81256 | 1216 | 0.1756 | 0.1756 | 0.175 | 0.2114 | thin resolution shells | 39.86 |
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] | |
5.6123 | 5.145 | -13.554 | 7.9417 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 3.88 |
t_other_torsion | 2.72 |
t_angle_deg | 1.12 |
t_bond_d | 0.014 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8916 |
Nucleic Acid Atoms | |
Solvent Atoms | 366 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
Auto-Rickshaw | phasing |
SHELXD | phasing |
SHELXE | model building |
RESOLVE | model building |
DM | model building |
ARP/wARP | model building |
BUSTER | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
RESOLVE | phasing |
DM | phasing |