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Human Transthyretin in Complex with 8-(3,5-dimethyl-1H-pyrazol-4-yl)quinoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294.15 100 mM HEPES, 200 mM CaCl2, 28% v/v PEG400, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.107 α = 90 b = 63.069 β = 90 c = 83.837 γ = 90
Symmetry Space Group P 21 2 21
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 APEX II CCD 2012-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.6 63.07 98.6 0.043 0.022 17.78 4.07 29346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.638 0.176 0.145
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 50.4 27814 1492 98.63 0.17925 0.17631 0.1895 0.23552 0.2444 RANDOM 15.248
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] 0.59 -0.37 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.108 r_sphericity_free 21.215 r_dihedral_angle_4_deg 16.734 r_sphericity_bonded 14.026 r_dihedral_angle_3_deg 13.366 r_dihedral_angle_1_deg 7.408 r_rigid_bond_restr 4.935 r_angle_refined_deg 1.962 r_angle_other_deg 0.859 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.108 r_sphericity_free 21.215 r_dihedral_angle_4_deg 16.734 r_sphericity_bonded 14.026 r_dihedral_angle_3_deg 13.366 r_dihedral_angle_1_deg 7.408 r_rigid_bond_restr 4.935 r_angle_refined_deg 1.962 r_angle_other_deg 0.859 r_chiral_restr 0.107 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1614 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing