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Protein-induced photophysical changes to the amyloid indicator dye, thioflavin T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIQ PDB ID 3CIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 5mM ThT, 50mM diammonium tartrate, 22.5% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.891 α = 90 b = 116.592 β = 90 c = 66.317 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2008-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.00 NSLS X25
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 50 97.7 0.127 0.127 6.5 23314 22778 11.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.769 87.4 0.922 0.922 1.68 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 3CIQ 2.7 20 19092 1035 98.85 0.23985 0.23896 0.2318 0.25637 0.2488 RANDOM 92.602
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] 10.52 -6.34 -4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_scangle_it 17.905 r_dihedral_angle_3_deg 17.226 r_scbond_it 14.142 r_dihedral_angle_4_deg 11.768 r_mcangle_it 11.069 r_mcbond_it 7.148 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.295 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.196 r_scangle_it 17.905 r_dihedral_angle_3_deg 17.226 r_scbond_it 14.142 r_dihedral_angle_4_deg 11.768 r_mcangle_it 11.069 r_mcbond_it 7.148 r_dihedral_angle_1_deg 6.702 r_angle_refined_deg 1.295 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5028 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 66
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling