X-RAY DIFFRACTION

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 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.739α = 90
b = 85.035β = 90
c = 65.093γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0000ALS5.0.2

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
11.525096.90.05815.46.6343193619017.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.521.5784.50.2570.2574.95.13096

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.5238.1936134181596.910.1620.160.188RANDOM15.582
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]
-0.36-0.691.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg14.147
r_sphericity_free9.977
r_scangle_it5.821
r_dihedral_angle_1_deg5.761
r_scbond_it4.638
r_sphericity_bonded4.347
r_mcangle_it3.116
r_rigid_bond_restr2.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.26
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg14.147
r_sphericity_free9.977
r_scangle_it5.821
r_dihedral_angle_1_deg5.761
r_scbond_it4.638
r_sphericity_bonded4.347
r_mcangle_it3.116
r_rigid_bond_restr2.959
r_mcbond_it2.583
r_angle_refined_deg1.772
r_angle_other_deg1.021
r_mcbond_other0.904
r_symmetry_vdw_refined0.312
r_symmetry_vdw_other0.22
r_nbd_refined0.213
r_nbd_other0.205
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.13
r_chiral_restr0.121
r_nbtor_other0.09
r_symmetry_hbond_refined0.078
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1880
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing