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Human Transthyretin in Complex with 4-(quinolin-8-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine
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 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.03 α = 90 b = 42.13 β = 90 c = 63.73 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 PIXEL DECTRIS PILATUS 6M 2012-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 1.27 42.51 99.1 0.051 0.015 22.5 13.1 60596
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 1.27 1.3 0.64 0.19 3.9
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 1.27 32.48 57487 3059 98.99 0.15189 0.14981 0.1553 0.19091 0.1925 RANDOM 19.482
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] -0.21 0.39 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.865 r_sphericity_free 25.233 r_dihedral_angle_4_deg 15.981 r_sphericity_bonded 15.401 r_dihedral_angle_3_deg 13.317 r_rigid_bond_restr 8.507 r_dihedral_angle_1_deg 6.295 r_angle_refined_deg 2.316 r_angle_other_deg 0.977 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.865 r_sphericity_free 25.233 r_dihedral_angle_4_deg 15.981 r_sphericity_bonded 15.401 r_dihedral_angle_3_deg 13.317 r_rigid_bond_restr 8.507 r_dihedral_angle_1_deg 6.295 r_angle_refined_deg 2.316 r_angle_other_deg 0.977 r_chiral_restr 0.133 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 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 1760 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing