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Crystal structure of horse spleen L-ferritin at -40deg 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 8 293.15 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
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 233.15 PIXEL RIGAKU HyPix-6000HE 2022-12-19 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) 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 22.245 99.5 0.062 0.069 0.029 0.998 14.7 4.9 34339
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 0.442 0.539 0.303 0.801 2.5
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 22.245 34319 1742 99.26 0.147 0.1453 0.1602 0.1752 0.1826 13.26
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 17.003 r_dihedral_angle_3_deg 14.047 r_lrange_it 6.626 r_lrange_other 6.626 r_dihedral_angle_2_deg 6.457 r_scangle_it 5.085 r_scangle_other 5.083 r_dihedral_angle_1_deg 4.992 r_scbond_it 3.22 r_scbond_other 3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.003 r_dihedral_angle_3_deg 14.047 r_lrange_it 6.626 r_lrange_other 6.626 r_dihedral_angle_2_deg 6.457 r_scangle_it 5.085 r_scangle_other 5.083 r_dihedral_angle_1_deg 4.992 r_scbond_it 3.22 r_scbond_other 3.22 r_mcangle_it 2.974 r_mcangle_other 2.973 r_mcbond_it 1.854 r_mcbond_other 1.844 r_angle_refined_deg 1.661 r_angle_other_deg 0.595 r_symmetry_metal_ion_refined 0.346 r_metal_ion_refined 0.304 r_nbd_refined 0.244 r_symmetry_nbd_refined 0.238 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.187 r_nbd_other 0.181 r_symmetry_nbd_other 0.166 r_symmetry_xyhbond_nbd_refined 0.145 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.074 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 190 Heterogen Atoms 27
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building