2FLM

Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (6 carbon linker)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMZPDB ENTRY 1BMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7pH 7.00, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1642.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.776α = 90
b = 84.605β = 90
c = 65.732γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAC Science DIP-20002002-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6522.1998.32903429034-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6451.68893.92

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 1BMZ1.6522.192903426140289497.770.201670.201670.198060.23396RANDOM21.03
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]
-1.040.510.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.198
r_dihedral_angle_4_deg18.589
r_dihedral_angle_3_deg15.438
r_dihedral_angle_1_deg5.733
r_scangle_it5.597
r_scbond_it4.044
r_mcangle_it2.596
r_angle_refined_deg2.297
r_mcbond_it2.146
r_angle_other_deg1.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.198
r_dihedral_angle_4_deg18.589
r_dihedral_angle_3_deg15.438
r_dihedral_angle_1_deg5.733
r_scangle_it5.597
r_scbond_it4.044
r_mcangle_it2.596
r_angle_refined_deg2.297
r_mcbond_it2.146
r_angle_other_deg1.975
r_mcbond_other0.534
r_symmetry_hbond_refined0.358
r_symmetry_vdw_other0.253
r_nbd_refined0.244
r_nbd_other0.227
r_xyhbond_nbd_refined0.201
r_symmetry_vdw_refined0.197
r_nbtor_refined0.189
r_chiral_restr0.141
r_nbtor_other0.099
r_bond_refined_d0.027
r_bond_other_d0.003
r_gen_planes_refined0.001
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1768
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms39

Software

Software
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement