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Crystal structure of horse spleen L-ferritin S118A 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 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.296 α = 90 b = 181.296 β = 90 c = 181.296 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 2022-08-02 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) 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 18.51 99.7 0.107 0.119 0.996 10.8 4.9 34030
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 1.072 1.272 0.467 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 18.51 34006 1724 99.505 0.173 0.171 0.1843 0.2033 0.2081 13.249
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 16.399 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_2_deg 7.074 r_lrange_it 6.622 r_lrange_other 6.416 r_dihedral_angle_1_deg 4.763 r_scangle_it 4.451 r_scangle_other 4.429 r_mcangle_it 2.899 r_mcangle_other 2.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.399 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_2_deg 7.074 r_lrange_it 6.622 r_lrange_other 6.416 r_dihedral_angle_1_deg 4.763 r_scangle_it 4.451 r_scangle_other 4.429 r_mcangle_it 2.899 r_mcangle_other 2.897 r_scbond_it 2.756 r_scbond_other 2.731 r_mcbond_it 1.792 r_mcbond_other 1.742 r_angle_refined_deg 1.568 r_angle_other_deg 0.556 r_symmetry_nbd_refined 0.379 r_symmetry_metal_ion_refined 0.372 r_metal_ion_refined 0.336 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.17 r_nbd_other 0.167 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.011 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 1392 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 32
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building