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Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and crystal contact tuned negatively supercharged ferritin variant Ftn(neg)-m1 (Mg formate condition)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CEI
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(Wildtype) added to coverslide in this order.
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.007 α = 90 b = 127.007 β = 90 c = 175.193 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 CdTe 16M 2020-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.55 72.1 97.7 0.161 0.046 0.997 8.3 12.1 391240
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 1.55 1.58 0.135 5.7
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 1.55 59.774 391211 16135 97.689 0.22 0.2185 0.2181 0.2413 0.2403 24.427
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] -0.518 -0.518 1.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 5.824 r_lrange_it 4.742 r_lrange_other 4.733 r_scangle_it 3.973 r_scangle_other 3.973 r_scbond_it 2.621 r_scbond_other 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 5.824 r_lrange_it 4.742 r_lrange_other 4.733 r_scangle_it 3.973 r_scangle_other 3.973 r_scbond_it 2.621 r_scbond_other 2.621 r_mcangle_it 2.213 r_mcangle_other 2.211 r_mcbond_it 1.687 r_mcbond_other 1.685 r_angle_refined_deg 1.471 r_angle_other_deg 1.399 r_nbd_refined 0.21 r_nbd_other 0.177 r_symmetry_nbd_refined 0.175 r_symmetry_nbd_other 0.166 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.106 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.067 r_metal_ion_refined 0.032 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17100 Nucleic Acid Atoms Solvent Atoms 976 Heterogen Atoms 38
Software Software Software Name Purpose xia2 data reduction XDS data scaling PHASER phasing Coot model building REFMAC refinement