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Crystal structure of horse spleen L-ferritin at -100deg 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 3.09 60.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.624 α = 90 b = 180.624 β = 90 c = 180.624 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 173.15 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 1.5420
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 23.526 99.7 0.099 0.109 0.046 0.997 10.6 5.2 34683
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 1.02 1.203 0.628 0.508 1.2
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 23.526 33628 1642 99.459 0.172 0.1714 0.185 0.1905 0.1975 14.372
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 17.077 r_dihedral_angle_3_deg 14.508 r_dihedral_angle_2_deg 7.084 r_lrange_it 6.616 r_lrange_other 6.594 r_scangle_it 4.772 r_dihedral_angle_1_deg 4.767 r_scangle_other 4.722 r_scbond_it 3.063 r_scbond_other 3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.077 r_dihedral_angle_3_deg 14.508 r_dihedral_angle_2_deg 7.084 r_lrange_it 6.616 r_lrange_other 6.594 r_scangle_it 4.772 r_dihedral_angle_1_deg 4.767 r_scangle_other 4.722 r_scbond_it 3.063 r_scbond_other 3.01 r_mcangle_other 2.476 r_mcangle_it 2.474 r_angle_refined_deg 1.622 r_mcbond_it 1.618 r_mcbond_other 1.617 r_angle_other_deg 0.599 r_symmetry_nbd_refined 0.329 r_nbd_refined 0.245 r_nbd_other 0.239 r_xyhbond_nbd_refined 0.226 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.168 r_metal_ion_refined 0.147 r_symmetry_metal_ion_refined 0.147 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.049 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 242 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building