6WCT
Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 287 | 33 mg/mL StmaA.01463.a.B1.PW38755 in 7 mM magnesium chloride, 7 mM ATP, 7 mM GMP (5GP) against MCSG1 screen condition B1 (0.6 M sodium chloride, 0.1 M MES, pH 6.5, 20% PEG4000), supplemented with 20% ethylene glycol as cryoprotectant, unique puck ID pfi1-7, crystal tracking ID 314557b1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.66 | α = 90 |
b = 101.42 | β = 92.03 |
c = 70.02 | 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 | RAYONIX MX300-HS | 2020-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.1 | 47.51 | 99.9 | 0.044 | 0.05 | 0.999 | 18.97 | 4.665 | 51005 | 48.413 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.1 | 2.15 | 100 | 0.578 | 0.652 | 0.903 | 2.98 | 4.688 |
Refinement
Statistics | |||||||||||||||||||
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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 (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3TR0 | 2.1 | 47.51 | 47846 | 2890 | 93.71 | 0.1822 | 0.1792 | 0.2294 | 57.0784 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6125 |
Nucleic Acid Atoms | |
Solvent Atoms | 286 |
Heterogen Atoms | 105 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |