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Crystal structure of horse spleen L-ferritin A115T mutant at -180deg 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 3.11 60.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.156 α = 90 b = 181.156 β = 90 c = 181.156 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 2023-01-19 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 1.5 23.596 100 0.072 0.078 0.028 0.999 19.7 7.4 41193
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 1.5 1.53 0.665 0.748 0.336 0.742 2.1
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 1.5 23.596 41171 1997 99.925 0.16 0.1591 0.1589 0.1808 0.1807 11.409
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 18.185 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_2_deg 12.195 r_lrange_it 6.305 r_lrange_other 6.012 r_dihedral_angle_1_deg 4.718 r_scangle_it 4.414 r_scangle_other 4.372 r_scbond_it 2.826 r_scbond_other 2.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.185 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_2_deg 12.195 r_lrange_it 6.305 r_lrange_other 6.012 r_dihedral_angle_1_deg 4.718 r_scangle_it 4.414 r_scangle_other 4.372 r_scbond_it 2.826 r_scbond_other 2.749 r_mcangle_it 2.645 r_mcangle_other 2.645 r_angle_refined_deg 1.767 r_mcbond_it 1.737 r_mcbond_other 1.708 r_angle_other_deg 0.631 r_symmetry_nbd_refined 0.38 r_metal_ion_refined 0.33 r_symmetry_metal_ion_refined 0.317 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.25 r_nbtor_refined 0.187 r_symmetry_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.153 r_nbd_other 0.148 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1395 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building