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Iron loaded human H-chain ferritin, anaerobic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M bicine pH 9.0
0.1 M sodium chloride
2 M magnesium chloride
60 mM ferrous chloride
3 mM sodium azide
Crystal Properties Matthews coefficient Solvent content 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.958 α = 90 b = 182.958 β = 90 c = 182.958 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 100 PIXEL DECTRIS PILATUS3 6M 2023-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.106 28.93 99.86 1 56.52 2 31515 26.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.106 2.181 0.979
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.11 28.93 1.35 28689 2882 99.95 0.1578 0.1541 0.1542 0.1913 0.1911 28.29
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 13.4827 f_angle_d 0.8174 f_chiral_restr 0.0422 f_bond_d 0.0067 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1424 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing