4PED
Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthes
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | Seeded microbatch experiment, 5 mg/mL protein 12.5% PEG 3350, 50 mM HEPES pH 7.5, 5 mM MgCl2, 150 mM Am2SO4, 0.15 mM TCEP, 5 microliter sitting drop in bridge of VDX plate, equilibrated against 12.5% PEG 3350, 50 mM HEPES pH 7.5, 150 mM Am2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 37.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 148.671 | α = 90 |
b = 54.557 | β = 94 |
c = 45.009 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 MX-300 | 2013-06-15 | 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) | 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 | 1.64 | 50 | 97 | 0.077 | 23 | 7.6 | 69420 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.64 | 1.67 | 94.8 | 0.893 | 1.5 | 5.6 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 1.64 | 36.634 | 1.38 | 69420 | 3478 | 80.09 | 0.1672 | 0.1649 | 0.211 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.844 |
f_angle_d | 1.433 |
f_chiral_restr | 0.06 |
f_bond_d | 0.012 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3128 |
Nucleic Acid Atoms | |
Solvent Atoms | 267 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
PHENIX | phasing |
ARP | model building |
PHENIX | model building |
PHENIX | refinement |