7Q9L

Transthyretin complexed with (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5298TTR:SB11 complex at 5.2mg/ml in 10mM sodium phosphate pH7.6 and 100mM potassium chloride was mixed 1:1 with 1.3-1.6M sodium citrate and 3.5% glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.2645.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.048α = 90
b = 64.749β = 90
c = 85.046γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2018-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.97993MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.4543.051000.0510.0540.0170.99922.110.54296219.152
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4799.91.3761.4440.4310.79910.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTin-house model1.4542.5640701219999.890.13440.13280.1633RANDOM25.327
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]
-0.741.56-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg14.394
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg6.399
r_rigid_bond_restr1.97
r_angle_refined_deg1.467
r_angle_other_deg1.389
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.86
r_dihedral_angle_4_deg14.394
r_dihedral_angle_3_deg12.782
r_dihedral_angle_1_deg6.399
r_rigid_bond_restr1.97
r_angle_refined_deg1.467
r_angle_other_deg1.389
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1756
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms47

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction