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Human transthyretin (TTR) complexed with Benzoxazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ PDB ENTRY 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1 MM EDTA, 100 mM KCL, 10 MM SODIUM R 0.35 M AMMONIUM SULFATE - CRYSTALS WERE SOAKED WITH THE INHIBITOR, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.072 α = 90 b = 84.69 β = 90 c = 64.731 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 4 2002-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90 APS 14-BM-C
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 1.54 35.36 86 0.05 30705 30705 -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) 1.54 1.58 89 0.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BMZ 1.541 35.36 30705 29158 1545 85.88 0.23 0.21885 0.21741 0.24629 RANDOM 21.487
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] 0.1 -0.11 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_3_deg 14.849 r_dihedral_angle_4_deg 10.585 r_dihedral_angle_1_deg 5.518 r_scangle_it 3.842 r_scbond_it 2.499 r_mcangle_it 1.775 r_angle_refined_deg 1.455 r_mcbond_it 1.042 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_3_deg 14.849 r_dihedral_angle_4_deg 10.585 r_dihedral_angle_1_deg 5.518 r_scangle_it 3.842 r_scbond_it 2.499 r_mcangle_it 1.775 r_angle_refined_deg 1.455 r_mcbond_it 1.042 r_nbtor_refined 0.31 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1752 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling EPMR phasing CNS refinement HKL-2000 data collection HKL-2000 data reduction