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Crystal structure of horse spleen L-ferritin at -180deg Celsius.
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 8 293 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.18 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.058 α = 90 b = 182.058 β = 90 c = 182.058 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 93.15 PIXEL RIGAKU HyPix-6000HE 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.542
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 18.581 99.6 0.054 1 26.8 10 41630
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.946
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 1.5 18.581 41564 2069 99.383 0.156 0.1549 0.1549 0.1743 0.1747 10.88
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 18.027 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_2_deg 7.491 r_lrange_it 5.907 r_lrange_other 5.572 r_dihedral_angle_1_deg 4.684 r_scangle_it 4.035 r_scangle_other 3.996 r_scbond_it 2.616 r_scbond_other 2.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.027 r_dihedral_angle_3_deg 13.628 r_dihedral_angle_2_deg 7.491 r_lrange_it 5.907 r_lrange_other 5.572 r_dihedral_angle_1_deg 4.684 r_scangle_it 4.035 r_scangle_other 3.996 r_scbond_it 2.616 r_scbond_other 2.548 r_mcangle_other 2.158 r_mcangle_it 2.157 r_angle_refined_deg 1.792 r_mcbond_it 1.396 r_mcbond_other 1.396 r_angle_other_deg 0.611 r_symmetry_nbd_refined 0.409 r_nbd_refined 0.247 r_symmetry_metal_ion_refined 0.227 r_xyhbond_nbd_refined 0.205 r_metal_ion_refined 0.193 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.163 r_nbd_other 0.147 r_symmetry_xyhbond_nbd_refined 0.145 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_symmetry_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 1393 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 46
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building