6WWD
Crystal structure of Nucleoside-triphosphatase / dITP/XTP pyrophosphatase from Mycobacterium abscessus ATCC 19977 / DSM 44196
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 290 | RigakuReagents, JCSG+ screen, condition a2: 20% PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: MyabA.00786.a.AE1.PS38631 at 26.62 mg/ml: tray 315036 a2, cryo: 20% ethylene glycol, puck rse0-4. For phasing, a crystal from the same well was soaked for 20sec in a solution made of 20% 2.5M sodium iodide in ethylene glycol and 80% reservoir, and then vitrified in liquid nitrogen: tray 315056 a2, puck fdv5-14 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.69 | α = 90 |
b = 104.04 | β = 90 |
c = 146.5 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU SATURN 944+ | RIGAKU VARIMAX HF | 2020-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
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 | 47.9 | 99.1 | 0.117 | 0.126 | 0.998 | 14.47 | 7.031 | 45678 | 26.991 |
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 | 98 | 0.411 | 0.45 | 0.891 | 4.62 | 6.082 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 2.1 | 47.9 | 1.35 | 45664 | 1961 | 99.04 | 0.1885 | 0.1861 | 0.2437 | 0 | 30.1091 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.816 |
f_angle_d | 0.932 |
f_chiral_restr | 0.056 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5518 |
Nucleic Acid Atoms | |
Solvent Atoms | 550 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SHELXDE | phasing |
PHASER | phasing |
ARP/wARP | model building |
Coot | model building |
PARROT | phasing |