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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 1KPR PDB ENTRY 1KPR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25% PEG 3350, 50mM diammonium tartrate, 5mM Thioflavin T, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.349 α = 90 b = 28.467 β = 91.42 c = 74.983 γ = 90
Symmetry Space Group P 1 21 1
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 2 1 x-ray
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 1.00 APS 24-ID-E 2 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 1.6 50 98.3 0.082 0.082 8.89 1.9 38793
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.83 88.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ENTRY 1KPR 1.6 29.27 20653 26034 1398 99.8 0.191 0.189 0.1946 0.223 0.2325 RANDOM 31.14
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] 0.07 0.05 -0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 13.336 r_dihedral_angle_1_deg 6.641 r_scangle_it 3.174 r_mcangle_it 2.889 r_scbond_it 2.077 r_mcbond_it 1.775 r_angle_refined_deg 1.542 r_angle_other_deg 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.171 r_dihedral_angle_4_deg 17.169 r_dihedral_angle_3_deg 13.336 r_dihedral_angle_1_deg 6.641 r_scangle_it 3.174 r_mcangle_it 2.889 r_scbond_it 2.077 r_mcbond_it 1.775 r_angle_refined_deg 1.542 r_angle_other_deg 1.12 r_mcbond_other 0.538 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1628 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 83
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling