1SN2

Crystal Structure of Sea Bream Transthyretin at 1.90A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F41Human transthyretin, pdb code 1F41

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5296PEG 1550 MME, sodium citrate, ammonium sulphate, nickel sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.497α = 90
b = 58.497β = 90
c = 140.71γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.755097.10.04746104
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)
11.751.8192.20.451

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 REPLACEMENTTHROUGHOUTHuman transthyretin, pdb code 1F411.7519.84461043974244391000.17830.178360.174890.20964RANDOM21.58
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]
-0.18-0.180.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.389
r_dihedral_angle_1_deg3.959
r_scangle_it2.757
r_scbond_it1.622
r_mcangle_it1.316
r_angle_refined_deg1.303
r_angle_other_deg0.718
r_mcbond_it0.695
r_symmetry_vdw_refined0.326
r_symmetry_vdw_other0.278
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.389
r_dihedral_angle_1_deg3.959
r_scangle_it2.757
r_scbond_it1.622
r_mcangle_it1.316
r_angle_refined_deg1.303
r_angle_other_deg0.718
r_mcbond_it0.695
r_symmetry_vdw_refined0.326
r_symmetry_vdw_other0.278
r_symmetry_hbond_refined0.259
r_nbd_refined0.228
r_nbd_other0.215
r_xyhbond_nbd_refined0.184
r_chiral_restr0.082
r_xyhbond_nbd_other0.049
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3529
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing