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X-ray structure of TRIL-encapsulated human heavy chain ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0 M magnesium chloride, 0.1 M bicine buffer pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.02 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.06 α = 90 b = 183.06 β = 90 c = 183.06 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 100 PIXEL DECTRIS PILATUS 6M 2022-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0001 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 105.69 99.9 0.2 0.059 0.998 0.711 20 12183
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 1.8 1 0.371 0.827 15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5n27 2.301 105.69 12183 603 99.787 0.173 0.1706 0.1756 0.2236 0.2198 34.08
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_2_deg 39.756 r_dihedral_angle_4_deg 18.124 r_dihedral_angle_3_deg 13.902 r_lrange_it 9.044 r_lrange_other 9.04 r_scangle_it 6.038 r_scangle_other 6.037 r_dihedral_angle_1_deg 5.896 r_mcangle_it 4.85 r_mcangle_other 4.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.756 r_dihedral_angle_4_deg 18.124 r_dihedral_angle_3_deg 13.902 r_lrange_it 9.044 r_lrange_other 9.04 r_scangle_it 6.038 r_scangle_other 6.037 r_dihedral_angle_1_deg 5.896 r_mcangle_it 4.85 r_mcangle_other 4.799 r_scbond_it 3.715 r_scbond_other 3.713 r_mcbond_it 3.017 r_mcbond_other 2.953 r_angle_refined_deg 1.422 r_angle_other_deg 1.386 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.178 r_nbd_other 0.167 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.126 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.079 r_metal_ion_refined 0.031 r_bond_refined_d 0.009 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 1424 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling PHASER phasing