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X-ray structure of human H-chain ferritin treated with SDS
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 3.07 59.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.92 α = 90 b = 183.92 β = 90 c = 183.92 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 2022-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.52 106.18 99.5 0.185 0.185 0.016 1 41.2 20 41266
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 1.52 1.55 100 0.859 2.4 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 1.52 106.18 41266 2056 99.489 0.153 0.1513 0.1644 0.1903 0.2004 22.741
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 38.741 r_dihedral_angle_4_deg 20.723 r_dihedral_angle_3_deg 13.037 r_lrange_it 8.141 r_lrange_other 7.75 r_dihedral_angle_1_deg 5.563 r_scangle_it 5.448 r_scangle_other 5.446 r_scbond_it 3.59 r_scbond_other 3.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.741 r_dihedral_angle_4_deg 20.723 r_dihedral_angle_3_deg 13.037 r_lrange_it 8.141 r_lrange_other 7.75 r_dihedral_angle_1_deg 5.563 r_scangle_it 5.448 r_scangle_other 5.446 r_scbond_it 3.59 r_scbond_other 3.588 r_mcangle_it 3.461 r_mcangle_other 3.445 r_mcbond_it 2.282 r_mcbond_other 2.25 r_angle_refined_deg 1.815 r_angle_other_deg 1.607 r_symmetry_xyhbond_nbd_refined 0.47 r_xyhbond_nbd_refined 0.269 r_nbd_refined 0.254 r_symmetry_xyhbond_nbd_other 0.244 r_nbd_other 0.183 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.176 r_symmetry_nbd_refined 0.176 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.059 r_symmetry_metal_ion_refined 0.015 r_bond_refined_d 0.014 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 1424 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing