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Human transthyretin (TTR) in complex with 3,5-Dimethyl-4-hydroxystilbene
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 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 298.0K
Crystal Properties Matthews coefficient Solvent content 2.15 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.022 α = 90 b = 85.56 β = 90 c = 64.52 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 ADSC QUANTUM 315 2007-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 1.51 50 99.6 0.044 34.6 6.8 37877 18
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) 1.51 1.56 99 0.227 7.3 6.1 22509
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 1.52 38.44 37307 1858 99.69 0.162 0.161 0.1695 0.189 0.1974 RANDOM 15.205
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] 0.09 -0.21 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 19.953 r_dihedral_angle_3_deg 13.424 r_sphericity_free 10.955 r_dihedral_angle_1_deg 5.998 r_scangle_it 5.891 r_sphericity_bonded 4.544 r_scbond_it 4.476 r_mcangle_it 3.19 r_mcbond_it 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 19.953 r_dihedral_angle_3_deg 13.424 r_sphericity_free 10.955 r_dihedral_angle_1_deg 5.998 r_scangle_it 5.891 r_sphericity_bonded 4.544 r_scbond_it 4.476 r_mcangle_it 3.19 r_mcbond_it 2.732 r_rigid_bond_restr 2.328 r_angle_refined_deg 1.731 r_angle_other_deg 0.937 r_mcbond_other 0.892 r_symmetry_hbond_refined 0.422 r_symmetry_vdw_other 0.211 r_nbd_refined 0.208 r_nbd_other 0.208 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.16 r_chiral_restr 0.119 r_nbtor_other 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1881 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing