2GZX
Crystal Structure of the TatD deoxyribonuclease MW0446 from Staphylococcus aureus. Northeast Structural Genomics Consortium Target ZR237.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 291 | 25% PEG 3350, 0.2 Ammonium acetate, 5 mM magnesium chloride, 0.1 M TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.678 | α = 90 |
b = 77.324 | β = 98.01 |
c = 76.129 | γ = 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 QUANTUM 4 | 2006-05-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97913 | NSLS | X4A |
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 | 2.2 | 26.79 | 99.8 | 0.102 | 4.4 | 53584 | 53477 | 18.8 |
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 | 2.2 | 2.28 | 0.548 | 4.3 | 5328 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.2 | 26.79 | 51275 | 2042 | 95.9 | 0.258 | 0.258 | 0.2619 | 0.286 | 0.2865 | RANDOM | 31.5 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
4.23 | 2.1 | -5.13 | 0.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.1 |
c_angle_deg | 1.6 |
c_improper_angle_d | 0.99 |
c_bond_d | 0.014 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4019 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
HKL-2000 | data scaling |
SOLVE | phasing |