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Crystal Structure of Transthyretin in Complex With Ligand C-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVQ PDB ENTRY 1DVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 POTASSIUM CHLORIDE, POTASSIUM PHOSPHATE, AMMONIUM SULFATE, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.813 α = 90 b = 42.838 β = 90 c = 64.644 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 120 IMAGE PLATE MARRESEARCH MIRRORS 2009-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 35.8 99.9 0.07 10.7 5.1 26484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 5.4 100 0.27 4 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1DVQ 1.7 23.79 23681 2589 97.56 0.22187 0.21815 0.2219 0.2572 0.2546 RANDOM 26.166
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] -0.66 0.53 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.286 r_dihedral_angle_4_deg 25.529 r_dihedral_angle_3_deg 16.57 r_scangle_it 6.846 r_dihedral_angle_1_deg 5.735 r_scbond_it 4.3 r_mcangle_it 3.001 r_angle_refined_deg 2.125 r_mcbond_it 1.729 r_chiral_restr 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.286 r_dihedral_angle_4_deg 25.529 r_dihedral_angle_3_deg 16.57 r_scangle_it 6.846 r_dihedral_angle_1_deg 5.735 r_scbond_it 4.3 r_mcangle_it 3.001 r_angle_refined_deg 2.125 r_mcbond_it 1.729 r_chiral_restr 0.16 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1780 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing