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The Structure of V122I Mutant Transthyretin in Complex with AG10
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 THE WT-TTR WAS CONCENTRATED TO 4 MG/ML IN 10 MM NAPI, 100 MM KCL, AT PH 7.6 AND CO-CRYSTALLIZED AT ROOM TEMPERATURE WITH INHIBITORS USING THE VAPOR-DIFFUSION SITTING DROP METHOD, CRYSTALS WERE GROWN FROM 1.395 M SODIUM CITRATE, 3.5% V/V GLYCEROL AT PH 5.5. THE CRYSTALS WERE FROZEN USING A CRYO-PROTECTANT SOLUTION OF 1.395 M SODIUM CITRATE, PH 5.5, CONTAINING 10% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.727 α = 90 b = 84.839 β = 90 c = 63.91 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 PIXEL DECTRIS PILATUS 6M Rh coated flat mirror 2012-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9797 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 1.18 63.91 98.6 0.022 34.5 6.1 75242 12.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.25 91 0.332 4.5 4.9 9986
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 1.18 63.91 75181 3769 98.5 0.1613 0.16 0.1655 0.186 0.1926 RANDOM 19.0955
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] 0.56 -0.18 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.906 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 6.257 r_scangle_it 5.66 r_scbond_it 3.857 r_mcangle_it 3.129 r_mcbond_it 1.972 r_angle_refined_deg 1.725 r_rigid_bond_restr 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.906 r_dihedral_angle_4_deg 20.531 r_dihedral_angle_3_deg 13.703 r_dihedral_angle_1_deg 6.257 r_scangle_it 5.66 r_scbond_it 3.857 r_mcangle_it 3.129 r_mcbond_it 1.972 r_angle_refined_deg 1.725 r_rigid_bond_restr 1.657 r_angle_other_deg 1.227 r_mcbond_other 0.571 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1787 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection autoXDS data reduction autoXDS data scaling PHASER phasing