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Human transthyretin (ttr) complexed with diflunisal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 5-7 mg/ml protein, in 0.3 M AMMONIUM SULFATE, 100 MM KCL, 1 MM EDTA, 10 MM SODIUM PHOSPHATE equilibrated against 2 M ammonium sulfate; SOAKED WITH THE INHIBITOR., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.204 α = 90 b = 85.265 β = 90 c = 64.208 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 2003-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 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 1.85 35.58 98.4 0.09 20478 20478
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.852 1.9 96.11
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BMZ 1.85 35.58 20477 19419 1058 98.15 0.21351 0.21351 0.21232 0.2186 0.23494 0.242 RANDOM 28.18
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.969 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_1_deg 5.75 r_scangle_it 2.96 r_scbond_it 2.142 r_angle_other_deg 2.084 r_mcangle_it 1.516 r_angle_refined_deg 1.412 r_mcbond_it 1.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.969 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_1_deg 5.75 r_scangle_it 2.96 r_scbond_it 2.142 r_angle_other_deg 2.084 r_mcangle_it 1.516 r_angle_refined_deg 1.412 r_mcbond_it 1.395 r_symmetry_vdw_refined 0.368 r_symmetry_vdw_other 0.329 r_chiral_restr 0.235 r_nbd_other 0.2 r_nbd_refined 0.189 r_nbtor_refined 0.183 r_mcbond_other 0.175 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling EPMR phasing CNS refinement