5N5Q

Human TTR altered conformation from soaking in iron chloride.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5K1J 

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: 27 % polyethylene glycol 4,000, 0.2 M imidazole malate, pH 6.0. cryosoak: 40% SM3 (, 25 % MPEG 5K, 25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 25 % MPEG 5K, 0.1 M CHC (citric acid, HEPES, CHES: 90 % acid /10 % basic), 30 mM FeCl2, 2 h soak.
Crystal Properties
Matthews coefficientSolvent content
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.73α = 90
b = 81.81β = 90
c = 69.46γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9Mmirrors2016-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 21.73915SOLEILPROXIMA 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
12.535099.20.20.1850.9968.2813.2115593-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.532.6895.31.981.820.30.8312.2

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 REPLACEMENTTHROUGHOUT5K1J2.5340.9811342799.450.195080.192050.25252RANDOM52.976
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]
-1.071.74-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg18.591
r_dihedral_angle_3_deg16.948
r_long_range_B_other12.248
r_long_range_B_refined12.223
r_scangle_other8.559
r_dihedral_angle_1_deg6.963
r_mcangle_it6.268
r_mcangle_other6.266
r_scbond_it5.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg18.591
r_dihedral_angle_3_deg16.948
r_long_range_B_other12.248
r_long_range_B_refined12.223
r_scangle_other8.559
r_dihedral_angle_1_deg6.963
r_mcangle_it6.268
r_mcangle_other6.266
r_scbond_it5.657
r_scbond_other5.654
r_mcbond_it3.852
r_mcbond_other3.851
r_angle_refined_deg1.604
r_angle_other_deg0.932
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms101
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing