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Crystal structure of ferritin mutant(E53H/E56H/E57H/R59H/E60H/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 3.14 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.639 α = 90 b = 181.639 β = 90 c = 181.639 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 2024-04-08 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) 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 1.5 22.23 99.3 0.085 0.092 0.033 0.997 17 7.2 41233
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 1.5 1.53 99.6 0.623 0.698 0.31 0.82 2.2 4.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 22.191 40813 2055 98.219 0.208 0.2066 0.2067 0.2251 0.225 10.649
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 36.592 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 12.331 r_lrange_it 5.83 r_lrange_other 5.626 r_dihedral_angle_1_deg 4.603 r_scangle_it 3.779 r_scangle_other 3.582 r_scbond_it 2.404 r_scbond_other 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.592 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 12.331 r_lrange_it 5.83 r_lrange_other 5.626 r_dihedral_angle_1_deg 4.603 r_scangle_it 3.779 r_scangle_other 3.582 r_scbond_it 2.404 r_scbond_other 2.266 r_mcangle_it 1.885 r_mcangle_other 1.885 r_angle_refined_deg 1.83 r_angle_other_deg 1.653 r_mcbond_it 1.203 r_mcbond_other 1.109 r_symmetry_metal_ion_refined 0.407 r_metal_ion_refined 0.358 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.257 r_symmetry_xyhbond_nbd_refined 0.214 r_nbd_other 0.207 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.177 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.014 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 1387 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 32
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building