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Crystal structure of horse spleen L-ferritin at 0deg Celsius.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.084 α = 90 b = 182.084 β = 90 c = 182.084 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 273.15 PIXEL RIGAKU HyPix-6000HE 2022-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 22.091 99.3 0.077 0.087 0.039 0.997 13.1 4.5 34317
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 96.7 0.901 1.102 0.622 0.46
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 1.6 22.091 34311 1738 99.045 0.157 0.155 0.1694 0.1864 0.1952 15.614
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 17.234 r_dihedral_angle_3_deg 14.731 r_lrange_it 7.527 r_lrange_other 7.328 r_dihedral_angle_2_deg 7.155 r_scangle_it 6.111 r_scangle_other 6.101 r_dihedral_angle_1_deg 4.948 r_scbond_it 3.947 r_scbond_other 3.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.234 r_dihedral_angle_3_deg 14.731 r_lrange_it 7.527 r_lrange_other 7.328 r_dihedral_angle_2_deg 7.155 r_scangle_it 6.111 r_scangle_other 6.101 r_dihedral_angle_1_deg 4.948 r_scbond_it 3.947 r_scbond_other 3.843 r_mcangle_it 2.637 r_mcangle_other 2.637 r_mcbond_it 1.729 r_mcbond_other 1.708 r_angle_refined_deg 1.648 r_angle_other_deg 0.582 r_symmetry_nbd_refined 0.308 r_nbd_refined 0.243 r_symmetry_metal_ion_refined 0.211 r_metal_ion_refined 0.196 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_other 0.17 r_nbd_other 0.14 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.011 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 1385 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building