1QWH

a covalent dimer of transthyretin that affects the amyloid pathway


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DVQPDB ENTRY 1DVQ.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.8298PEG 4000, 0.2 M Magnesium Nitrate , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.63α = 90
b = 86.05β = 90
c = 63.83γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (ho rizontal focusing)2003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97945SSRLBL9-2

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
11.363092.40.05324.53.84841148411-3
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)
11.3629.8896.90.5392.83.7

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 1DVQ.pdb1.3629.884841148380242792.340.215710.215340.22246RANDOM14.855
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]
-0.12-0.190.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.987
r_angle_refined_deg1.56
r_nbd_refined0.207
r_symmetry_hbond_refined0.156
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.102
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.987
r_angle_refined_deg1.56
r_nbd_refined0.207
r_symmetry_hbond_refined0.156
r_symmetry_vdw_refined0.151
r_xyhbond_nbd_refined0.102
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1674
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing