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Crystal structure of human Transthyretin (TTR) at pH3.5
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 3.5 289 5-7 mg/ml protein, 0.1 M sodium acetate, 20 % PEG 3350, 0.3-0.5 M ammonium sulfate equilibrated against 2.0M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.124 α = 90 b = 85.494 β = 90 c = 62.419 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 2003-07-24 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 1.63 35.58 98.2 0.054 19.36 29348 29348
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) 1.63 1.65 88.6 0.69 2.69
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 PDB ENTRY 1BMZ 1.7 35.58 24412 24412 1314 98.49 0.22472 0.22472 0.22284 0.2216 0.26048 0.2586 RANDOM 23.883
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 -0.19 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.846 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_4_deg 9.807 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.914 r_scbond_it 1.738 r_mcangle_it 1.251 r_angle_refined_deg 1.081 r_mcbond_it 0.749 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.846 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_4_deg 9.807 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.914 r_scbond_it 1.738 r_mcangle_it 1.251 r_angle_refined_deg 1.081 r_mcbond_it 0.749 r_nbtor_refined 0.304 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1609 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose EPMR phasing REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling