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Crystal structure of Ferritin mutant(E53H/E57H)
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 3.2 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.681 α = 90 b = 182.681 β = 90 c = 182.681 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 2022-11-22 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) 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 23.81 99.4 0.102 0.996 16.1 7.2 42036
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.66 0.697 0.769 0.796 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 23.783 41621 2100 98.507 0.22 0.2189 0.219 0.2409 0.2409 12.354
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 36.519 r_dihedral_angle_4_deg 21.142 r_dihedral_angle_3_deg 12.716 r_lrange_it 6.283 r_lrange_other 5.989 r_dihedral_angle_1_deg 4.505 r_scangle_other 3.628 r_scangle_it 3.621 r_scbond_it 2.327 r_scbond_other 2.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 21.142 r_dihedral_angle_3_deg 12.716 r_lrange_it 6.283 r_lrange_other 5.989 r_dihedral_angle_1_deg 4.505 r_scangle_other 3.628 r_scangle_it 3.621 r_scbond_it 2.327 r_scbond_other 2.317 r_mcangle_it 1.816 r_mcangle_other 1.812 r_angle_refined_deg 1.707 r_angle_other_deg 1.6 r_mcbond_it 1.123 r_mcbond_other 1.096 r_symmetry_nbd_refined 0.393 r_nbd_refined 0.254 r_metal_ion_refined 0.24 r_symmetry_metal_ion_refined 0.217 r_xyhbond_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.167 r_nbd_other 0.162 r_symmetry_xyhbond_nbd_other 0.097 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_xyhbond_nbd_other 0.068 r_bond_refined_d 0.012 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 1389 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 20
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building