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Crystal structure of horse spleen L-ferritin at -80deg 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 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.016 α = 90 b = 182.016 β = 90 c = 182.016 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 193.15 PIXEL RIGAKU HyPix-6000HE 2022-12-20 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 23.7 99.6 0.108 0.122 0.055 0.993 10 4.7 34413
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 1.6 1.63 0.365
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 22.752 34410 1746 99.416 0.178 0.1761 0.1886 0.2094 0.2141 13.688
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 16.642 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_2_deg 6.902 r_lrange_it 6.858 r_lrange_other 6.481 r_scangle_it 4.963 r_dihedral_angle_1_deg 4.828 r_scangle_other 4.643 r_scbond_it 3.113 r_scbond_other 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.642 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_2_deg 6.902 r_lrange_it 6.858 r_lrange_other 6.481 r_scangle_it 4.963 r_dihedral_angle_1_deg 4.828 r_scangle_other 4.643 r_scbond_it 3.113 r_scbond_other 2.927 r_mcangle_other 2.511 r_mcangle_it 2.51 r_mcbond_it 1.63 r_angle_refined_deg 1.598 r_mcbond_other 1.555 r_angle_other_deg 0.562 r_metal_ion_refined 0.545 r_symmetry_metal_ion_refined 0.545 r_symmetry_nbd_refined 0.438 r_xyhbond_nbd_refined 0.253 r_nbd_refined 0.248 r_nbd_other 0.217 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_other 0.164 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1385 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 32
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building