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Crystal structure of Horse spleen L-ferritin mutant (R52F/E56F/R59F/E63F) with Nile Red
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 Ammonium sulfate, Cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.552 α = 90 b = 181.552 β = 90 c = 181.552 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 PIXEL RIGAKU HyPix-6000HE 2021-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54184
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 1.65 19.03 99.9 0.077 0.081 0.025 0.999 22.1 10.1 31335
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 1.65 1.68 100 0.847 0.92 0.356 0.823 2.1 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1DAT 1.65 19.03 1.33 30993 1565 98.89 0.1918 0.1908 0.1911 0.2094 0.2091
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 f_dihedral_angle_d 13.727 f_angle_d 1.784 f_chiral_restr 0.09 f_plane_restr 0.019 f_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1378 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 38
Software Software Software Name Purpose CrysalisPro data collection CrysalisPro data reduction Aimless data scaling MOLREP phasing REFMAC refinement Coot model building