4TQP

Human transthyretin (TTR) complexed with (R)-3-(9H-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide in a dual binding mode


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TQI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7293Protein: 5 mg/ml in 0.05 M NaCl, 0.05 M sodium acetate, pH 5.5. Precipitant: 60% (30% PEG-4K, 0.2 M imidazole malate, pH 6.0) and 40% (MPEG-5K, 0.1 M sodium acetate, pH 5.5). Cryoprotectant: 40% (25 % diethylene glycol, 12.5 % MPD, 37.5 % 2,3-butanediol, 12.5 % 1,4-dioxane), 12.5% MPEG 5K, 25% MPEG 550, 0.1 M (sodium propionate, sodium cacodylate, Bis-Tris-propane: 50% component A pH 4; 50% B pH 9.5) with 1 milli-M ligand.
Crystal Properties
Matthews coefficientSolvent content
2.1442.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.121α = 90
b = 86.081β = 90
c = 63.473γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.87006ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.5851.199.90.1250.11814.129.193312533100-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6499.91.879.5

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 REPLACEMENTTHROUGHOUT4TQI1.5851.0931425167499.920.144410.141480.19761RANDOM19.98
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]
0.19-0.210.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.429
r_dihedral_angle_4_deg18.643
r_dihedral_angle_3_deg14.398
r_scangle_it7.776
r_dihedral_angle_1_deg6.799
r_scbond_it5.449
r_mcangle_it4.253
r_rigid_bond_restr2.867
r_mcbond_it2.728
r_angle_refined_deg2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.429
r_dihedral_angle_4_deg18.643
r_dihedral_angle_3_deg14.398
r_scangle_it7.776
r_dihedral_angle_1_deg6.799
r_scbond_it5.449
r_mcangle_it4.253
r_rigid_bond_restr2.867
r_mcbond_it2.728
r_angle_refined_deg2.15
r_chiral_restr0.157
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1792
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
XDSdata scaling
XSCALEdata scaling
ADSCdata collection