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Human transthyretin (TTR) in complex with 3,5-Dibromo-4-hydroxybiphenyl
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 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.058 α = 90 b = 85.215 β = 90 c = 64.811 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 99.4 0.058 23.2 7 37389 18.1
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) 1.52 1.56 100 0.203 11.6 6.8 25064
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 38.43 37259 1859 99.4 0.167 0.165 0.1734 0.197 0.2005 RANDOM 15.32
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] -0.12 0.58 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.423 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 13.535 r_sphericity_free 10.156 r_dihedral_angle_1_deg 6.047 r_scangle_it 5.854 r_scbond_it 4.66 r_sphericity_bonded 4.597 r_mcangle_it 3.086 r_mcbond_it 2.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.423 r_dihedral_angle_4_deg 19.381 r_dihedral_angle_3_deg 13.535 r_sphericity_free 10.156 r_dihedral_angle_1_deg 6.047 r_scangle_it 5.854 r_scbond_it 4.66 r_sphericity_bonded 4.597 r_mcangle_it 3.086 r_mcbond_it 2.549 r_rigid_bond_restr 2.42 r_angle_refined_deg 1.728 r_angle_other_deg 1.007 r_mcbond_other 0.988 r_nbd_refined 0.21 r_nbd_other 0.203 r_symmetry_vdw_other 0.202 r_symmetry_vdw_refined 0.187 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.104 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1877 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 30
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