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Crystal structure of horse spleen L-ferritin at -180deg Celsius cooled from -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 3.1 60.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.76 α = 90 b = 180.76 β = 90 c = 180.76 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 2022-12-19 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 24.167 98.2 0.09 0.1 0.042 0.997 11.4 5 33140
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 0.642 0.766 0.411 0.72 1.6
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 24.167 33129 1626 97.7 0.17 0.1684 0.1818 0.2015 0.2128 11.158
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 18.072 r_dihedral_angle_3_deg 14.535 r_dihedral_angle_2_deg 6.404 r_lrange_it 5.93 r_lrange_other 5.93 r_dihedral_angle_1_deg 5.088 r_scangle_it 3.851 r_scangle_other 3.849 r_scbond_it 2.459 r_scbond_other 2.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.072 r_dihedral_angle_3_deg 14.535 r_dihedral_angle_2_deg 6.404 r_lrange_it 5.93 r_lrange_other 5.93 r_dihedral_angle_1_deg 5.088 r_scangle_it 3.851 r_scangle_other 3.849 r_scbond_it 2.459 r_scbond_other 2.457 r_mcangle_it 2.31 r_mcangle_other 2.31 r_angle_refined_deg 1.605 r_mcbond_it 1.592 r_mcbond_other 1.467 r_angle_other_deg 0.586 r_symmetry_nbd_refined 0.334 r_nbd_refined 0.24 r_nbd_other 0.22 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_other 0.169 r_symmetry_metal_ion_refined 0.138 r_metal_ion_refined 0.113 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.01 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 254 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building