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Structure of transthyretin in complex with the kinetic stabilizer 201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 WT-TTR at 4 mg/mL and five-fold molar excess compound 201 crystallized from solution containing 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. Crystals cryoprotected by addition of 10% (v/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.265 α = 90 b = 85.467 β = 90 c = 64.285 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 CCD MARMOSAIC 325 mm CCD 2006-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.99184 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 50 99.7 0.041 28.7 4 47590 16.6
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 1.4 1.45 100 0.555 2.4 3.9
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 2FBR 1.4 33.1 45137 2409 99.6 0.13429 0.13256 0.1288 0.16721 0.1635 RANDOM 22.235
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] 0.27 1.07 -1.34
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.155 r_dihedral_angle_2_deg 35.095 r_sphericity_bonded 22.112 r_dihedral_angle_4_deg 17.858 r_dihedral_angle_3_deg 12.679 r_rigid_bond_restr 9.336 r_dihedral_angle_1_deg 6.199 r_angle_refined_deg 1.891 r_angle_other_deg 0.871 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.155 r_dihedral_angle_2_deg 35.095 r_sphericity_bonded 22.112 r_dihedral_angle_4_deg 17.858 r_dihedral_angle_3_deg 12.679 r_rigid_bond_restr 9.336 r_dihedral_angle_1_deg 6.199 r_angle_refined_deg 1.891 r_angle_other_deg 0.871 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing DENZO data reduction