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Human Transthyretin in Complex with 4-(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 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.06 α = 90 b = 42.3 β = 90 c = 64.77 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 1.21 35.55 98.9 0.05 0.019 19.2 8.4 70465
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 1.21 1.25 0.61 0.291
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 1.21 35.55 66868 3553 98.76 0.15513 0.15366 0.1568 0.18339 0.185 RANDOM 16.173
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] -0.1 0.15 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.342 r_sphericity_free 15.494 r_dihedral_angle_3_deg 12.086 r_sphericity_bonded 10.814 r_rigid_bond_restr 8.423 r_dihedral_angle_4_deg 8.18 r_dihedral_angle_1_deg 6.406 r_long_range_B_refined 4.663 r_long_range_B_other 4.662 r_scangle_other 4.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.342 r_sphericity_free 15.494 r_dihedral_angle_3_deg 12.086 r_sphericity_bonded 10.814 r_rigid_bond_restr 8.423 r_dihedral_angle_4_deg 8.18 r_dihedral_angle_1_deg 6.406 r_long_range_B_refined 4.663 r_long_range_B_other 4.662 r_scangle_other 4.625 r_scbond_it 4.042 r_scbond_other 4.041 r_mcangle_other 3.675 r_mcangle_it 3.624 r_mcbond_it 2.904 r_mcbond_other 2.902 r_angle_refined_deg 2.175 r_angle_other_deg 0.957 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1694 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing