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Crystal structure of ferritin mutantFr-H8 (R52H/E53H/E56H/E57H/R59H/E60H/E63H/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 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 3.16 61.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.999 α = 90 b = 181.999 β = 90 c = 181.999 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 22.26 99.5 0.093 0.099 0.032 0.997 17.3 9.4 41576
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 1.6 100 0.881 0.96 0.376 0.797 2.1 6.8
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 22.235 41384 2089 99.107 0.217 0.2158 0.2249 0.2424 0.2484 13.528
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 37.843 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 13.138 r_lrange_it 5.851 r_lrange_other 5.616 r_dihedral_angle_1_deg 4.764 r_scangle_it 4.09 r_scangle_other 3.863 r_scbond_it 2.578 r_scbond_other 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.843 r_dihedral_angle_4_deg 19.426 r_dihedral_angle_3_deg 13.138 r_lrange_it 5.851 r_lrange_other 5.616 r_dihedral_angle_1_deg 4.764 r_scangle_it 4.09 r_scangle_other 3.863 r_scbond_it 2.578 r_scbond_other 2.42 r_mcangle_it 2.161 r_mcangle_other 2.16 r_angle_refined_deg 1.767 r_angle_other_deg 1.636 r_mcbond_it 1.315 r_mcbond_other 1.314 r_nbd_refined 0.261 r_symmetry_nbd_refined 0.217 r_xyhbond_nbd_refined 0.196 r_nbd_other 0.183 r_nbtor_refined 0.182 r_symmetry_nbd_other 0.174 r_symmetry_xyhbond_nbd_refined 0.169 r_chiral_restr 0.095 r_metal_ion_refined 0.09 r_symmetry_nbtor_other 0.086 r_symmetry_metal_ion_refined 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 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 1391 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 23
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building