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X-ray structure of Auoxo4-encapsulated horse spleen apoferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ERK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.6-0.8 M (NH4)2SO4, 0.1 M Tris pH 7.4-7.7, 50-60 mM CdSO4
Crystal Properties Matthews coefficient Solvent content 3.1 60.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.878 α = 90 b = 180.878 β = 90 c = 180.878 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 CCD RIGAKU SATURN 944 2016-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.6 104.43 99 0.187 0.145 5.4 4 8209
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.414 0.404
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ERK 2.6 104.43 7811 391 98.9 0.186 0.184 0.236 0.2617 RANDOM 23.6
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 36.663 r_dihedral_angle_3_deg 17.144 r_dihedral_angle_4_deg 15.646 r_long_range_B_refined 6.956 r_long_range_B_other 6.954 r_dihedral_angle_1_deg 5.95 r_scangle_other 4.306 r_mcangle_it 3.153 r_mcangle_other 3.151 r_scbond_it 2.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.663 r_dihedral_angle_3_deg 17.144 r_dihedral_angle_4_deg 15.646 r_long_range_B_refined 6.956 r_long_range_B_other 6.954 r_dihedral_angle_1_deg 5.95 r_scangle_other 4.306 r_mcangle_it 3.153 r_mcangle_other 3.151 r_scbond_it 2.513 r_scbond_other 2.499 r_mcbond_other 1.768 r_mcbond_it 1.767 r_angle_refined_deg 1.474 r_angle_other_deg 0.963 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1385 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing