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Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (6 carbon linker)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ PDB ENTRY 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 pH 7.00, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.776 α = 90 b = 84.605 β = 90 c = 65.732 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 MAC Science DIP-2000 2002-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 22.19 98.3 29034 29034 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.645 1.688 93.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BMZ 1.65 22.19 29034 26140 2894 97.77 0.20167 0.20167 0.19806 0.23396 RANDOM 21.03
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] -1.04 0.51 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.198 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.438 r_dihedral_angle_1_deg 5.733 r_scangle_it 5.597 r_scbond_it 4.044 r_mcangle_it 2.596 r_angle_refined_deg 2.297 r_mcbond_it 2.146 r_angle_other_deg 1.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.198 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.438 r_dihedral_angle_1_deg 5.733 r_scangle_it 5.597 r_scbond_it 4.044 r_mcangle_it 2.596 r_angle_refined_deg 2.297 r_mcbond_it 2.146 r_angle_other_deg 1.975 r_mcbond_other 0.534 r_symmetry_hbond_refined 0.358 r_symmetry_vdw_other 0.253 r_nbd_refined 0.244 r_nbd_other 0.227 r_xyhbond_nbd_refined 0.201 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.189 r_chiral_restr 0.141 r_nbtor_other 0.099 r_bond_refined_d 0.027 r_bond_other_d 0.003 r_gen_planes_refined 0.001 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1768 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 39
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement