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Crystal structure of ferritin mutant (E53H/E57H/E60H/R64H)
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 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 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.93 α = 90 b = 180.93 β = 90 c = 180.93 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 2022-04-25 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) 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 20.24 99.9 0.072 0.033 0.999 21.4 8.9 41042
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 99.8 0.608 0.671 0.276 0.819 2.8 5.7
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 1.501 20.237 40955 1988 99.905 0.157 0.1564 0.1703 0.1706 0.1836 10.43
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_6_deg 17.862 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_2_deg 9.032 r_lrange_it 6.446 r_lrange_other 6.198 r_dihedral_angle_1_deg 4.602 r_scangle_it 3.944 r_scangle_other 3.796 r_scbond_it 2.578 r_scbond_other 2.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.862 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_2_deg 9.032 r_lrange_it 6.446 r_lrange_other 6.198 r_dihedral_angle_1_deg 4.602 r_scangle_it 3.944 r_scangle_other 3.796 r_scbond_it 2.578 r_scbond_other 2.401 r_mcangle_it 2.373 r_mcangle_other 2.372 r_angle_refined_deg 1.957 r_mcbond_it 1.414 r_mcbond_other 1.39 r_angle_other_deg 0.659 r_symmetry_nbd_refined 0.352 r_symmetry_metal_ion_refined 0.347 r_metal_ion_refined 0.257 r_nbd_refined 0.252 r_symmetry_xyhbond_nbd_refined 0.21 r_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.172 r_nbd_other 0.168 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1399 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 48
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building