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Human transthyretin (TTR) in complex with 3,5-Dibromo-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 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.739 α = 90 b = 85.035 β = 90 c = 65.093 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 Mirrors 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 1.52 50 96.9 0.058 15.4 6.6 34319 36190 17.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.52 1.57 84.5 0.257 0.257 4.9 5.1 3096
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.52 38.19 36134 1815 96.91 0.162 0.16 0.188 0.2131 RANDOM 15.582
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] -0.36 -0.69 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 14.147 r_sphericity_free 9.977 r_scangle_it 5.821 r_dihedral_angle_1_deg 5.761 r_scbond_it 4.638 r_sphericity_bonded 4.347 r_mcangle_it 3.116 r_rigid_bond_restr 2.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.26 r_dihedral_angle_4_deg 17.649 r_dihedral_angle_3_deg 14.147 r_sphericity_free 9.977 r_scangle_it 5.821 r_dihedral_angle_1_deg 5.761 r_scbond_it 4.638 r_sphericity_bonded 4.347 r_mcangle_it 3.116 r_rigid_bond_restr 2.959 r_mcbond_it 2.583 r_angle_refined_deg 1.772 r_angle_other_deg 1.021 r_mcbond_other 0.904 r_symmetry_vdw_refined 0.312 r_symmetry_vdw_other 0.22 r_nbd_refined 0.213 r_nbd_other 0.205 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.121 r_nbtor_other 0.09 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1880 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 34
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing