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Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and reduced charge negatively supercharged ferritin variant Ftn(neg)-m3 (Mg formate condition)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CEI Human Heavy Chain Ferritin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 reservoir: 0.19M Magnesium FormateFtn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaClFtn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(neg)-m3 added to coverslide in this order.
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.039 α = 90 b = 127.039 β = 90 c = 176.961 γ = 90
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 EIGER2 X 16M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.99 49.356 99.9 0.037 0.052 0.037 0.999 12.1 2 188549
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 2.03 0.392 0.555 0.392 0.749 2
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 1.999 49.356 188548 9438 99.872 0.183 0.1814 0.1807 0.2207 0.2204 34.171
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] -0.898 -0.898 1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.968 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 13.932 r_lrange_other 8.812 r_lrange_it 8.802 r_dihedral_angle_1_deg 5.881 r_scangle_it 5.614 r_scangle_other 5.614 r_scbond_it 3.732 r_scbond_other 3.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.968 r_dihedral_angle_4_deg 19.79 r_dihedral_angle_3_deg 13.932 r_lrange_other 8.812 r_lrange_it 8.802 r_dihedral_angle_1_deg 5.881 r_scangle_it 5.614 r_scangle_other 5.614 r_scbond_it 3.732 r_scbond_other 3.732 r_mcangle_it 3.642 r_mcangle_other 3.639 r_mcbond_it 2.698 r_mcbond_other 2.693 r_angle_refined_deg 1.546 r_angle_other_deg 1.434 r_nbd_refined 0.219 r_nbd_other 0.206 r_symmetry_nbd_refined 0.203 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.158 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.078 r_xyhbond_nbd_other 0.047 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17107 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 24
Software Software Software Name Purpose xia2 data scaling XDS data scaling Aimless data scaling PHASER phasing Coot model building REFMAC refinement