3B56

Crystal structure of transthyretin in complex with 3,5-diiodosalicylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F86PDB ENTRY 1F86

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5287200mM acetate buffer, 2.2M ammonium sulfate, 7% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.1342.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.539α = 90
b = 85.757β = 90
c = 64.346γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.5528.5899.90.05215.23.634993349582

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1F861.5527.3433166175699.910.190430.189170.21368RANDOM14.518
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]
0.14-0.390.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.567
r_dihedral_angle_4_deg17.553
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg5.551
r_scangle_it3.281
r_scbond_it2.105
r_mcangle_it1.49
r_angle_refined_deg1.271
r_mcbond_it0.789
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.567
r_dihedral_angle_4_deg17.553
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg5.551
r_scangle_it3.281
r_scbond_it2.105
r_mcangle_it1.49
r_angle_refined_deg1.271
r_mcbond_it0.789
r_nbtor_refined0.31
r_symmetry_vdw_refined0.285
r_nbd_refined0.202
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.132
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1786
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing