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Crystal structure of horse spleen L-ferritin at -20deg 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, HANGING DROP 293.15 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.18 61.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.34 α = 90 b = 182.34 β = 90 c = 182.34 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 253.15 PIXEL RIGAKU HyPix-6000HE 2022-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5420
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 22.286 98.9 0.065 0.073 0.031 0.998 15.6 4.7 34348
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 0.605 0.732 0.404 0.708 1.9
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 22.286 34339 1712 98.684 0.149 0.1477 0.1477 0.1687 0.1687 14.359
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 17.256 r_dihedral_angle_3_deg 15.096 r_dihedral_angle_2_deg 8.046 r_lrange_it 7.744 r_lrange_other 7.743 r_scangle_it 6.073 r_scangle_other 6.07 r_dihedral_angle_1_deg 5.196 r_scbond_it 4.019 r_scbond_other 4.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.256 r_dihedral_angle_3_deg 15.096 r_dihedral_angle_2_deg 8.046 r_lrange_it 7.744 r_lrange_other 7.743 r_scangle_it 6.073 r_scangle_other 6.07 r_dihedral_angle_1_deg 5.196 r_scbond_it 4.019 r_scbond_other 4.017 r_mcangle_it 3.251 r_mcangle_other 3.249 r_mcbond_it 2.223 r_mcbond_other 2.204 r_angle_refined_deg 1.714 r_angle_other_deg 0.61 r_symmetry_nbd_refined 0.346 r_symmetry_metal_ion_refined 0.28 r_metal_ion_refined 0.271 r_nbd_refined 0.242 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_other 0.169 r_xyhbond_nbd_refined 0.144 r_nbd_other 0.13 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.071 r_bond_refined_d 0.012 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 1385 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building