5EZP

Human transthyretin (TTR) complexed with 4-hydroxy-chalcone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein: 5mg/ML in 0.05 M NaCl, 0.025 M Na acetate, pH 5.5 and 0.001 M 4-hydroxychalcone Reservoir: 30% PEG4K, 0.1M Tris-HCl, pH 8.5 4 boosts (5 M NaCl) Cryoprotectant: CryoSol SM1, 25% PEG 4K, 0.1 M (Na acetate, ADA, Bicine) Buffer 20% acid / 80% basic 0.01 M ligand.
Crystal Properties
Matthews coefficientSolvent content
2.5151.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.48α = 90
b = 62.48β = 90
c = 238.32γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rconvex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.55099.50.210.198.525.53580635643-3
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)
12.52.6597.81.721.155.15

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 REPLACEMENTTHROUGHOUT4PMF2.544.7233860178399.560.211730.209970.24467RANDOM50.257
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]
-1.14-0.57-1.143.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg22.141
r_dihedral_angle_3_deg16.771
r_long_range_B_refined7.533
r_long_range_B_other7.533
r_dihedral_angle_1_deg6.299
r_scangle_other4.455
r_mcangle_it4.002
r_mcangle_other4.001
r_scbond_it2.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.66
r_dihedral_angle_4_deg22.141
r_dihedral_angle_3_deg16.771
r_long_range_B_refined7.533
r_long_range_B_other7.533
r_dihedral_angle_1_deg6.299
r_scangle_other4.455
r_mcangle_it4.002
r_mcangle_other4.001
r_scbond_it2.669
r_scbond_other2.669
r_mcbond_it2.314
r_mcbond_other2.313
r_angle_other_deg2.302
r_angle_refined_deg1.895
r_chiral_restr0.101
r_bond_refined_d0.018
r_bond_other_d0.014
r_gen_planes_refined0.012
r_gen_planes_other0.012
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7257
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building