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Crystal structure of Horse spleen L-ferritin mutant (E53F/E56F/E57F/R59F/E60F/E63F) with Nile Red
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 Ammonium sulfate, Cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.511 α = 90 b = 181.511 β = 90 c = 181.511 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 2021-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54184
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 1.6 17.8 99.9 0.055 0.057 0.017 1 29.8 10 34271
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 1.6 1.63 100 0.513 0.559 0.217 0.904 3.4 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1DAT 1.6 17.799 34121 1708 99.429 0.165 0.164 0.1778 0.1858 0.1968 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_6_deg 16.999 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_2_deg 9.131 r_lrange_it 5.345 r_lrange_other 5.343 r_dihedral_angle_1_deg 4.81 r_scangle_it 3.993 r_scangle_other 3.991 r_scbond_it 2.648 r_scbond_other 2.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.999 r_dihedral_angle_3_deg 12.919 r_dihedral_angle_2_deg 9.131 r_lrange_it 5.345 r_lrange_other 5.343 r_dihedral_angle_1_deg 4.81 r_scangle_it 3.993 r_scangle_other 3.991 r_scbond_it 2.648 r_scbond_other 2.646 r_mcangle_it 2.341 r_mcangle_other 2.34 r_angle_refined_deg 1.953 r_mcbond_it 1.509 r_mcbond_other 1.487 r_angle_other_deg 0.684 r_symmetry_metal_ion_refined 0.446 r_metal_ion_refined 0.367 r_symmetry_nbd_refined 0.331 r_nbd_refined 0.245 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.169 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.135 r_symmetry_xyhbond_nbd_refined 0.115 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.076 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 1380 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 48
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building