2B9A

Human transthyretin (TTR) complexed with diflunisal analogues- TTR.3',5'-difluorobiphenyl-4-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 DROP7298ammonium sulfate, 100 mM KCL, 1 mM EDTA, 10 mM sodium phosphate, 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 = 42.935α = 90
b = 84.852β = 90
c = 63.742γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCCD-PXL-L6002002-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D1.0APS14-BM-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5442.18950.033374133741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.698

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BMZ1.5442.183374133720169395.70.230990.222340.24593RANDOM
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
r_dihedral_angle_2_deg32.202
r_dihedral_angle_3_deg15.82
r_dihedral_angle_4_deg15.3
r_dihedral_angle_1_deg6.68
r_scangle_it4.113
r_scbond_it2.829
r_angle_refined_deg2.724
r_mcangle_it2.014
r_mcbond_it1.265
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.202
r_dihedral_angle_3_deg15.82
r_dihedral_angle_4_deg15.3
r_dihedral_angle_1_deg6.68
r_scangle_it4.113
r_scbond_it2.829
r_angle_refined_deg2.724
r_mcangle_it2.014
r_mcbond_it1.265
r_nbtor_refined0.319
r_symmetry_hbond_refined0.264
r_symmetry_vdw_refined0.248
r_nbd_refined0.238
r_xyhbond_nbd_refined0.184
r_chiral_restr0.123
r_bond_refined_d0.067
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1718
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms34

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling