- PDB-5i35: Structure of the Human mitochondrial kinase COQ8A R611K with AMPP... -
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Basic information
Entry
Database: PDB / ID: 5i35
Title
Structure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia and Ubiquinone Deficiency Through Loss of Unorthodox Kinase Activity)
Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: One part of ADCK3 R611K, 0.2 mM, AMPPNP 2 mM, MgCl2, 4mM, mixed with an equal volume of sodium polyacrylate 5100, 26%; magnesium chloride, 20 mM; HEPES, 100 mM, pH 7.5
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.96862 Å / Relative weight: 1
Reflection
Resolution: 2.3→50 Å / Num. obs: 19840 / % possible obs: 100 % / Redundancy: 7.37 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.5
Reflection shell
Resolution: 2.3→2.36 Å / Redundancy: 7.61 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.65 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0135
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.3→44.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.075 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25887
1556
7.8 %
RANDOM
Rwork
0.18346
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obs
0.18952
18275
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK