3IMR

Transthyretin in complex with (E)-2,6-dibromo-4-(2,6-dichlorostyryl)phenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QGBpdb entry 2QGB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5298The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.927α = 90
b = 85.002β = 90
c = 64.506γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 325 mm CCDFlat collimating mirror, double crystal monochromator, toroid focusing mirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9194SSRLBL9-2

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
11.764.5599.50.05734.6142690323.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.71.76970.6957.311.92588

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 REPLACEMENTTHROUGHOUTpdb entry 2QGB1.75026562133399.560.1720.1690.217RANDOM27.504
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]
1.18-0.72-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.117
r_dihedral_angle_4_deg17.51
r_dihedral_angle_3_deg14.69
r_sphericity_free10.749
r_dihedral_angle_1_deg5.988
r_scangle_it5.86
r_sphericity_bonded5.544
r_rigid_bond_restr5.136
r_scbond_it4.646
r_mcangle_it3.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.117
r_dihedral_angle_4_deg17.51
r_dihedral_angle_3_deg14.69
r_sphericity_free10.749
r_dihedral_angle_1_deg5.988
r_scangle_it5.86
r_sphericity_bonded5.544
r_rigid_bond_restr5.136
r_scbond_it4.646
r_mcangle_it3.06
r_mcbond_it2.563
r_angle_refined_deg1.818
r_angle_other_deg0.927
r_mcbond_other0.921
r_nbd_other0.203
r_nbd_refined0.196
r_symmetry_vdw_refined0.191
r_nbtor_refined0.186
r_symmetry_hbond_refined0.183
r_symmetry_vdw_other0.168
r_xyhbond_nbd_refined0.163
r_chiral_restr0.109
r_nbtor_other0.092
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1863
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing