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Crystal structure of horse-spleen L-ferritin fused with amyloid beta peptide (1-42).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 Ammonium sulfate (0.5-1.0M), Cadmium sulfate (12-20 mM)
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.935 α = 90 b = 181.935 β = 90 c = 181.935 γ = 90
Symmetry Space Group F 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93.1 PIXEL RIGAKU HyPix-6000HE 2023-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2 21.691 97.7 0.996 19.8 7.4 17564
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.977
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 21.691 17554 913 97.414 0.217 0.2152 0.2267 0.2581 0.2629 13.437
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.112 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_2_deg 9.106 r_lrange_it 6.897 r_lrange_other 6.722 r_dihedral_angle_1_deg 6.058 r_scangle_other 5.669 r_scangle_it 5.662 r_scbond_other 3.554 r_scbond_it 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.112 r_dihedral_angle_3_deg 15.958 r_dihedral_angle_2_deg 9.106 r_lrange_it 6.897 r_lrange_other 6.722 r_dihedral_angle_1_deg 6.058 r_scangle_other 5.669 r_scangle_it 5.662 r_scbond_other 3.554 r_scbond_it 3.553 r_mcangle_it 3.031 r_mcangle_other 3.031 r_mcbond_it 1.954 r_mcbond_other 1.954 r_angle_refined_deg 1.938 r_angle_other_deg 0.653 r_symmetry_nbd_refined 0.301 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.19 r_symmetry_nbd_other 0.182 r_symmetry_metal_ion_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.153 r_nbd_other 0.15 r_metal_ion_refined 0.139 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.066 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1370 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building