2B77

Human transthyretin (TTR) complexed with Diflunisal analogues- TTR.2',4'-DICHLORO-4-HYDROXY-1,1'-BIPHENYL-3-CARBOXYLIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMZpdb entry 1bmz

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72981 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate - crystals were soaked with the inhibitor, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.215α = 90
b = 85.082β = 90
c = 64.401γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCCD-PXL-L6002003-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.541

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
11.751.399.940.070.0716.942548525485

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1bmz1.751.32548625485135099.940.209850.209850.20830.23845RANDOM20.4
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]
-0.04-0.090.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.24
r_dihedral_angle_3_deg15.762
r_dihedral_angle_4_deg14.526
r_dihedral_angle_1_deg6.933
r_scangle_it4.657
r_scbond_it3.298
r_angle_refined_deg2.361
r_mcbond_it2.215
r_mcangle_it2.147
r_angle_other_deg0.961
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.24
r_dihedral_angle_3_deg15.762
r_dihedral_angle_4_deg14.526
r_dihedral_angle_1_deg6.933
r_scangle_it4.657
r_scbond_it3.298
r_angle_refined_deg2.361
r_mcbond_it2.215
r_mcangle_it2.147
r_angle_other_deg0.961
r_symmetry_vdw_refined0.335
r_mcbond_other0.311
r_symmetry_vdw_other0.302
r_symmetry_hbond_refined0.238
r_xyhbond_nbd_refined0.225
r_nbd_other0.207
r_nbd_refined0.201
r_nbtor_refined0.184
r_chiral_restr0.094
r_nbtor_other0.088
r_gen_planes_other0.059
r_gen_planes_refined0.031
r_bond_refined_d0.022
r_bond_other_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1752
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing