5LLL

Crystal structure of DACM wild type Transthyretin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GKO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2 M CaCl2 0.1 M HEPES sodium pH 7.5 28% v/v PEG 400
Crystal Properties
Matthews coefficientSolvent content
1.8934.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.68α = 90
b = 64.49β = 90
c = 85.27γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 S 6MToroidal mirror2015-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.984003ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.4222.3599.30.0978.1545907
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.599.20.732.15

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 REPLACEMENTTHROUGHOUT1GKO1.4222.3543621222399.120.162310.159580.21693RANDOM23.389
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]
1.15-0.67-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free22.327
r_sphericity_bonded15.573
r_rigid_bond_restr6.372
r_scangle_other5.649
r_long_range_B_refined5.328
r_long_range_B_other5.171
r_scbond_other4.987
r_scbond_it4.978
r_mcangle_other3.7
r_mcangle_it3.692
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free22.327
r_sphericity_bonded15.573
r_rigid_bond_restr6.372
r_scangle_other5.649
r_long_range_B_refined5.328
r_long_range_B_other5.171
r_scbond_other4.987
r_scbond_it4.978
r_mcangle_other3.7
r_mcangle_it3.692
r_mcbond_it3.002
r_mcbond_other2.968
r_angle_refined_deg1.683
r_angle_other_deg0.846
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1785
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing