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Crystal structure of ferritin mutant (R52H/E56H/R59H/E63H)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Precipitant: (NH4)2SO4 (0.5-1.0M), CdSO4(12-20mM)
Protein: 15-20mg/ml
Crystallization drop: 1:1
Crystal Properties Matthews coefficient Solvent content 3.15 60.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.7 α = 90 b = 181.7 β = 90 c = 181.7 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 93 PIXEL RIGAKU HyPix-6000HE 2022-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.543
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.5 23.67 100 0.088 0.095 0.998 18.1 7.1 41552
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.6 0.673 0.468 0.76 2.1
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 1.5 23.655 41498 2111 99.8 0.169 0.1683 0.1684 0.1868 0.1871 10.7
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 37.975 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 11.604 r_lrange_it 5.843 r_lrange_other 5.572 r_dihedral_angle_1_deg 4.678 r_scangle_it 3.662 r_scangle_other 3.559 r_scbond_it 2.432 r_scbond_other 2.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.975 r_dihedral_angle_4_deg 19.952 r_dihedral_angle_3_deg 11.604 r_lrange_it 5.843 r_lrange_other 5.572 r_dihedral_angle_1_deg 4.678 r_scangle_it 3.662 r_scangle_other 3.559 r_scbond_it 2.432 r_scbond_other 2.276 r_mcangle_it 1.901 r_mcangle_other 1.9 r_angle_refined_deg 1.759 r_angle_other_deg 1.637 r_mcbond_it 1.15 r_mcbond_other 1.14 r_symmetry_nbd_refined 0.291 r_nbd_refined 0.254 r_symmetry_xyhbond_nbd_refined 0.234 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.189 r_nbtor_refined 0.182 r_symmetry_nbd_other 0.173 r_symmetry_metal_ion_refined 0.119 r_chiral_restr 0.106 r_metal_ion_refined 0.104 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 30
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building