5K1N

Human TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K1J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 + 3.6% polyethylene glycol monomethyl ether (MPEG5K), 30 mM sodium acetate pH 5.5 cryosoak: 40% SM3 (25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 50% PEG 8K and 0.5 milli-M of rhenium tris-carbonyl Pyta-C12 derivative.
Crystal Properties
Matthews coefficientSolvent content
2.2946.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.65α = 90
b = 82.13β = 90
c = 67.72γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9Mmirrors2016-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 21.175919SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.815098.20.0650.0520.99812.312.641147-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8698.40.7821.692.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5K1J1.8141.0651.2641116205098.10.19060.18880.2239
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.269
f_angle_d0.819
f_chiral_restr0.056
f_plane_restr0.006
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1785
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms31

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing