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Human Transthyretin in Complex with Isoquinolin-3-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 2.14 42.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.64 α = 90 b = 42.5 β = 90 c = 64.93 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 1.47 35.75 99.8 0.055 0.017 22.7 12.8 41047
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 1.47 1.51 0.662 0.215
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 1.47 35.75 38944 2059 99.77 0.16441 0.16174 0.1675 0.21508 0.2198 RANDOM 19.272
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] -0.08 0.22 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 21.384 r_sphericity_free 17.515 r_dihedral_angle_3_deg 12.846 r_sphericity_bonded 12.017 r_rigid_bond_restr 7.313 r_dihedral_angle_1_deg 5.857 r_scangle_other 4.758 r_long_range_B_refined 4.677 r_long_range_B_other 4.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 21.384 r_sphericity_free 17.515 r_dihedral_angle_3_deg 12.846 r_sphericity_bonded 12.017 r_rigid_bond_restr 7.313 r_dihedral_angle_1_deg 5.857 r_scangle_other 4.758 r_long_range_B_refined 4.677 r_long_range_B_other 4.675 r_scbond_it 4.389 r_scbond_other 4.387 r_mcangle_it 3.977 r_mcangle_other 3.975 r_mcbond_it 3.461 r_mcbond_other 3.365 r_angle_refined_deg 1.819 r_angle_other_deg 0.866 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1682 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing