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Crystal structure of horse spleen L-ferritin at -180deg Celsius cooled from -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 8 293.15 Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)
Crystal Properties Matthews coefficient Solvent content 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.786 α = 90 b = 180.786 β = 90 c = 180.786 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 2022-11-08 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 22.096 99.1 0.112 0.126 0.056 0.995 8.8 4.7 33540
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 0.955 1.162 0.649 0.53 1.1
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 22.096 33494 1649 98.799 0.181 0.1797 0.1909 0.2058 0.2139 12.117
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 17.932 r_dihedral_angle_3_deg 14.132 r_dihedral_angle_2_deg 8.959 r_lrange_it 6.243 r_lrange_other 6.243 r_dihedral_angle_1_deg 4.968 r_scangle_it 4.1 r_scangle_other 4.098 r_scbond_it 2.586 r_scbond_other 2.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.932 r_dihedral_angle_3_deg 14.132 r_dihedral_angle_2_deg 8.959 r_lrange_it 6.243 r_lrange_other 6.243 r_dihedral_angle_1_deg 4.968 r_scangle_it 4.1 r_scangle_other 4.098 r_scbond_it 2.586 r_scbond_other 2.585 r_mcangle_it 2.456 r_mcangle_other 2.456 r_angle_refined_deg 1.563 r_mcbond_it 1.561 r_mcbond_other 1.561 r_angle_other_deg 0.566 r_symmetry_nbd_refined 0.37 r_symmetry_metal_ion_refined 0.334 r_metal_ion_refined 0.29 r_nbd_refined 0.249 r_symmetry_xyhbond_nbd_other 0.244 r_nbd_other 0.226 r_symmetry_xyhbond_nbd_refined 0.206 r_xyhbond_nbd_refined 0.205 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_other 0.09 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.073 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 250 Heterogen Atoms 40
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building