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Unitary crystal structure of positively supercharged ferritin variant Ftn(pos)-m1 (Mg Formate condition)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 reservoir: 0.19M Magnesium Formate
Ftn(pos)-m1: 4 mg/mL in 50mM Tris pH 7.5 0.9 M NaCl
2microliter reservoir + 1microliter Ftn(pos)-m1 +1 microliterL 50mM Tris pH 7.5 0.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.898 α = 90 b = 126.898 β = 90 c = 187.468 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 EIGER X 16M 2021-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97625 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.75 105.09 98.9 0.174 0.193 0.082 0.997 8.3 10.5 145913
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 1.75 1.78 3.671 4.335 2.24 0.184 6.4
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 2 105.086 99602 4906 99.991 0.162 0.1603 0.1604 0.1925 0.1591 26.449
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] 0.545 0.545 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.117 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_2_deg 9.773 r_lrange_it 7.412 r_lrange_other 7.371 r_scangle_it 6.464 r_scangle_other 6.463 r_dihedral_angle_1_deg 5.605 r_scbond_it 4.165 r_scbond_other 4.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.117 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_2_deg 9.773 r_lrange_it 7.412 r_lrange_other 7.371 r_scangle_it 6.464 r_scangle_other 6.463 r_dihedral_angle_1_deg 5.605 r_scbond_it 4.165 r_scbond_other 4.165 r_mcangle_it 3.366 r_mcangle_other 3.366 r_mcbond_it 2.39 r_mcbond_other 2.383 r_angle_refined_deg 1.507 r_angle_other_deg 0.514 r_nbd_refined 0.229 r_nbtor_refined 0.185 r_metal_ion_refined 0.182 r_nbd_other 0.178 r_symmetry_nbd_other 0.168 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.12 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8568 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data scaling xia2 data scaling MOLREP phasing