5DWP

Crystal Structure of human transthyretin (TTR) processed with the CrystalDirect automated mounting and cryo-cooling technology


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PVL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium citrate, 1.6 M ammonium sulfate, pH=5.0
Crystal Properties
Matthews coefficientSolvent content
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.346α = 90
b = 62.521β = 90
c = 85.427γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.9765APS21-ID-D

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
11.219.63970.0688.24.569740
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.26

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 REPLACEMENTTHROUGHOUT4PVL1.219.6366062343199.220.164220.162570.19559RANDOM17.953
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]
-0.550.93-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.509
r_sphericity_free23.157
r_dihedral_angle_4_deg14.27
r_dihedral_angle_3_deg13.166
r_sphericity_bonded9.309
r_dihedral_angle_1_deg6.315
r_rigid_bond_restr5.658
r_long_range_B_refined4.952
r_long_range_B_other4.673
r_scangle_other4.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.509
r_sphericity_free23.157
r_dihedral_angle_4_deg14.27
r_dihedral_angle_3_deg13.166
r_sphericity_bonded9.309
r_dihedral_angle_1_deg6.315
r_rigid_bond_restr5.658
r_long_range_B_refined4.952
r_long_range_B_other4.673
r_scangle_other4.51
r_scbond_it3.837
r_scbond_other3.835
r_angle_other_deg2.496
r_mcangle_other2.419
r_mcangle_it2.392
r_mcbond_it1.847
r_mcbond_other1.832
r_angle_refined_deg1.732
r_chiral_restr0.098
r_gen_planes_other0.015
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.002
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 Atoms1792
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing