3RK0
X-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with AMP from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR23
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | micro batch under oil | 7.5 | 291 | Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, 0.02% NaN3, and 10mM dephospho-coenzyme A. Reservoir solution: 20% (w/v) PEG3350 and 200mM magnesium formate., micro batch under oil, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.201 | α = 90 |
b = 85.201 | β = 90 |
c = 74.249 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | MAR CCD 165 mm | mirrors | 2008-07-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4C | 0.97915 | NSLS | X4C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.4 | 30 | 99.7 | 0.07 | 0.059 | 46.8 | 15 | 20451 | 20390 | 27.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.49 | 100 | 0.362 | 0.341 | 8.2 | 15.1 | 2031 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3RJZ | 2.4 | 19.94 | 2 | 2 | 20396 | 18724 | 1789 | 91.8 | 0.232 | 0.229 | 0.229 | 0.278 | RANDOM | 47.1 |
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] | |
2.47 | 2.47 | -4.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.9 |
c_angle_deg | 1 |
c_improper_angle_d | 0.66 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1688 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
COMO | phasing |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |