6LZI
Aquifex aeolicus MutL ATPase domain complexed with ADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5X9Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 50 mM tris-HCl, 50 mM NaCl, 5 mM MgCl2, 5 mM ADP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.017 | α = 80.978 |
b = 42.906 | β = 71.521 |
c = 53.845 | γ = 77.707 |
Symmetry | |
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Space Group | P 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 MX225HE | 2018-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.0000 | SPring-8 | BL38B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 1.69 | 50 | 92 | 0.064 | 0.041 | 0.78 | 24.3 | 11.2 | 29323 | 26.9081865961 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.69 | 1.73 | 94.9 | 0.75 | 0.43 | 1.86 | 7.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5x9y | 1.69105685009 | 41.7270024284 | 263.488974409 | 26762 | 1824 | 82.8365369734 | 0.205044957344 | 0.202383292 | 0.242574382921 | 38.2810646356 |
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 | 22.076271053 |
f_angle_d | 1.73326204268 |
f_chiral_restr | 0.125374078001 |
f_bond_d | 0.0159577013596 |
f_plane_restr | 0.00954226411044 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1961 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data processing |
HKL-2000 | data scaling |
PHENIX | phasing |
Coot | model building |
PHENIX | model building |
HKL-2000 | data reduction |