4QYA

Crystal structure of human transthyretin variant V30M in complex with luteolin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298V30M-TTR CONCENTRATION WAS 5 MG/ML IN 10 MM SODIUMPHOSPHATE, PH 7.6, 100 MM POTASSIUMCLORIDE. V30M-TTR WAS CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH 5 MOLAR EXCESS OF LUTEOLIN IN 3.5% V/V GLYCEROL AND 1.3-1.6 M SODIUM CITRATE AT PH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.894α = 90
b = 85.854β = 90
c = 63.685γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352014-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.72499.50.04543.38.4265242.51
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)
11.71.7695.90.316.1

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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 DIFFRACTIONMOLREP1.723.8061.3426481133899.480.16430.16250.1975
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_d14.765
f_angle_d1.102
f_chiral_restr0.074
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1794
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms43

Software

Software
Software NamePurpose
MOLREPphasing
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling