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Crystal structure of horse spleen L-ferritin A115V 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 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.749 α = 90 b = 181.749 β = 90 c = 181.749 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 293.15 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 1.541838
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 1.5 30.721 100 0.075 0.088 0.999 13.8 7.1 41611
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 1.5 1.53 0.742 0.836 0.806
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1DAT 1.5 30.721 41568 2119 99.868 0.161 0.1601 0.1602 0.1769 0.1765 12.033
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 17.927 r_dihedral_angle_3_deg 13.959 r_lrange_it 6.422 r_lrange_other 6.421 r_dihedral_angle_2_deg 4.697 r_dihedral_angle_1_deg 4.574 r_scangle_it 4.208 r_scangle_other 4.207 r_scbond_it 2.704 r_scbond_other 2.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.927 r_dihedral_angle_3_deg 13.959 r_lrange_it 6.422 r_lrange_other 6.421 r_dihedral_angle_2_deg 4.697 r_dihedral_angle_1_deg 4.574 r_scangle_it 4.208 r_scangle_other 4.207 r_scbond_it 2.704 r_scbond_other 2.703 r_mcangle_it 2.594 r_mcangle_other 2.593 r_angle_refined_deg 1.678 r_mcbond_it 1.57 r_mcbond_other 1.563 r_angle_other_deg 0.6 r_symmetry_nbd_refined 0.307 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.161 r_nbd_other 0.149 r_metal_ion_refined 0.145 r_symmetry_metal_ion_refined 0.145 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.012 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 1395 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing Coot model building