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Iron containing ferritin at 1.43A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 A 20 uL pellet of 50 mM cadmium sulfate in 2% agar was deposited on a cover slip. Adjacent to this was positioned ferritin (10 ul of 50 mg/ml ferritin, Sigma F4503) and precipitant (10 ul of 3.5M Ammonium Sulfate and 100 mM Tris pH 7.4). The cover slip was equilibrated over 3.5 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.21 61.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.59 α = 90 b = 181.59 β = 90 c = 181.59 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 EIGER X 9M 2018-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.43 50 99.14 31.81 138.2 45041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.47 100 48.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1IER 1.43 50 45041 2291 99.14 0.15792 0.15716 0.1638 0.1717 0.178 RANDOM 30.055
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_2_deg 35.427 r_dihedral_angle_4_deg 21.854 r_dihedral_angle_3_deg 13.755 r_long_range_B_refined 8.691 r_long_range_B_other 8.11 r_scangle_other 7.913 r_scbond_it 4.851 r_scbond_other 4.85 r_dihedral_angle_1_deg 4.46 r_mcangle_other 3.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.427 r_dihedral_angle_4_deg 21.854 r_dihedral_angle_3_deg 13.755 r_long_range_B_refined 8.691 r_long_range_B_other 8.11 r_scangle_other 7.913 r_scbond_it 4.851 r_scbond_other 4.85 r_dihedral_angle_1_deg 4.46 r_mcangle_other 3.004 r_mcangle_it 2.997 r_angle_refined_deg 2.646 r_mcbond_it 2.403 r_mcbond_other 2.376 r_angle_other_deg 1.911 r_chiral_restr 0.153 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1365 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing