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Human Transthyretin in Complex with 5-(quinolin-8-yl)pyrimidin-2-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 2.09 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.074 α = 90 b = 85.045 β = 90 c = 64.267 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-F 2013-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29
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 1.24 50 96.7 0.045 0.023 14.07 4.6 63682
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 1.24 1.272 0.592 0.327 1.83
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 1.24 35.46 60444 3208 96.25 0.16112 0.15944 0.163 0.19264 0.1923 RANDOM 17.365
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] 0.06 -0.1 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.399 r_sphericity_free 17.747 r_dihedral_angle_3_deg 10.475 r_sphericity_bonded 10.203 r_dihedral_angle_4_deg 8.956 r_rigid_bond_restr 6.985 r_dihedral_angle_1_deg 5.787 r_long_range_B_refined 4.199 r_long_range_B_other 4.198 r_scangle_other 3.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.399 r_sphericity_free 17.747 r_dihedral_angle_3_deg 10.475 r_sphericity_bonded 10.203 r_dihedral_angle_4_deg 8.956 r_rigid_bond_restr 6.985 r_dihedral_angle_1_deg 5.787 r_long_range_B_refined 4.199 r_long_range_B_other 4.198 r_scangle_other 3.691 r_mcangle_it 3.666 r_mcangle_other 3.665 r_scbond_it 3.3 r_scbond_other 3.298 r_mcbond_it 2.815 r_mcbond_other 2.814 r_angle_refined_deg 1.981 r_angle_other_deg 0.902 r_chiral_restr 0.137 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing