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X-ray structure of Auoxo3-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 7.4 293 Crystals of Auoxo3-encapsulated AFt with diamond-like morphology, suitable for X-ray diffraction data collection, were grown by hanging-drop vapor diffusion technique at 293 K mixing the protein (5-10 mg x mL-1) with equal volumes of a reservoir solution consisting of 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 3.09 60.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.645 α = 90 b = 180.645 β = 90 c = 180.645 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+ mirrors 2015-11-17 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) 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 1.85 104.3 99.5 0.237 0.243 0.102 0.666 9.2 6.9 20893 19.8
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 1.85 1.88 95 0.284 0.8 3.4
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 5ERK 1.85 104.3 20893 1128 99.5 0.18256 0.18024 0.1907 0.22596 0.2348 RANDOM 19.717
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 36.712 r_dihedral_angle_4_deg 22.694 r_dihedral_angle_3_deg 15.329 r_long_range_B_refined 7.912 r_long_range_B_other 7.106 r_dihedral_angle_1_deg 6.413 r_scangle_other 4.403 r_mcangle_other 3.138 r_mcangle_it 3.134 r_scbond_it 2.821
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.712 r_dihedral_angle_4_deg 22.694 r_dihedral_angle_3_deg 15.329 r_long_range_B_refined 7.912 r_long_range_B_other 7.106 r_dihedral_angle_1_deg 6.413 r_scangle_other 4.403 r_mcangle_other 3.138 r_mcangle_it 3.134 r_scbond_it 2.821 r_scbond_other 2.804 r_mcbond_it 1.97 r_mcbond_other 1.96 r_angle_refined_deg 1.752 r_angle_other_deg 0.932 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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 1385 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing