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Binary crystal structure of positively supercharged ferritin variant Ftn(pos) and native(K86Q) human heavy chain ferritin (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 Formate
Ftn(pos): 4 mg/mL in 50mM Tris pH 7.5 1 M NaCl
Ftn(Wildtype): 4mg/mL in 50mM Tris pH 7.5 0.3 M NaCl
2 uL reservoir + 1uL Ftn(pos) + 1uL Ftn(Wildtype) added to coverslide in this order.
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.802 α = 90 b = 126.802 β = 90 c = 175.598 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 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) 1.0332 PETRA III, EMBL c/o DESY P14 (MX2)
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 2 49.061 99.9 0.173 0.187 0.07 0.998 10.2 13.9 186148
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 1.164 1.257 0.473 0.824 13.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.001 49.061 186147 9313 99.924 0.205 0.2032 0.202 0.2468 0.2449 Random 30.915
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] -0.816 -0.816 1.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.597 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 14.715 r_lrange_other 7.294 r_lrange_it 7.288 r_dihedral_angle_1_deg 6.144 r_scangle_it 4.72 r_scangle_other 4.72 r_mcangle_it 3.413 r_mcangle_other 3.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.597 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 14.715 r_lrange_other 7.294 r_lrange_it 7.288 r_dihedral_angle_1_deg 6.144 r_scangle_it 4.72 r_scangle_other 4.72 r_mcangle_it 3.413 r_mcangle_other 3.413 r_scbond_it 3.091 r_scbond_other 3.091 r_mcbond_it 2.494 r_mcbond_other 2.491 r_angle_refined_deg 1.509 r_angle_other_deg 1.366 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.192 r_nbd_other 0.187 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.119 r_symmetry_xyhbond_nbd_other 0.097 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.078 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 17070 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data scaling xia2 data scaling MOLREP phasing