5K1J

Human TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 cryosoak: 40% SM2 (12.5 % ethylene glycol, 12.5 % glycerol, 12.5 % 1,2-propanediol, 25 % DMSO and 37.5% 1,4-dioxane) 50% PEG 8K and 0.2 milli-M of rhenium tris-carbonyl Pyta-C8 derivative.
Crystal Properties
Matthews coefficientSolvent content
2.2946.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.82α = 90
b = 83.1β = 90
c = 65.34γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors2016-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 21.175919SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
11.695099.10.0330.028122.923.4549863-3
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)
11.691.7492.40.6312.222.88

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 REPLACEMENTTHROUGHOUT4PME1.6941.5525309133299.590.173910.171340.22199RANDOM30.101
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]
-1.07-0.141.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.315
r_dihedral_angle_4_deg20.511
r_dihedral_angle_3_deg15.686
r_long_range_B_refined10.625
r_long_range_B_other10.623
r_scangle_other7.589
r_dihedral_angle_1_deg6.537
r_scbond_it4.957
r_scbond_other4.955
r_mcangle_it4.578
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.315
r_dihedral_angle_4_deg20.511
r_dihedral_angle_3_deg15.686
r_long_range_B_refined10.625
r_long_range_B_other10.623
r_scangle_other7.589
r_dihedral_angle_1_deg6.537
r_scbond_it4.957
r_scbond_other4.955
r_mcangle_it4.578
r_mcangle_other4.577
r_mcbond_it3.202
r_mcbond_other3.169
r_angle_refined_deg2.027
r_angle_other_deg1.057
r_chiral_restr0.15
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1792
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing