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X-ray structure of carboplatin-encapsulated horse spleen apoferritin (rotating anode data)
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 7.7 298 0.8 M (NH4)2SO4,
0.1 M Tris pH 7.7,
60 mM CdSO4.
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.654 α = 90 b = 180.654 β = 90 c = 180.654 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 2015-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.96 104.3 99.9 0.107 6.2 6.9 18700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2 100 0.489 3.8 5.2
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 1.96 104.3 17792 904 99.88 0.14847 0.14623 0.1601 0.19161 0.2025 RANDOM 20.803
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 37.81 r_dihedral_angle_4_deg 24.43 r_dihedral_angle_3_deg 14.998 r_long_range_B_refined 7.612 r_long_range_B_other 7.61 r_dihedral_angle_1_deg 5.637 r_scangle_other 4.523 r_scbond_it 2.887 r_scbond_other 2.872 r_mcangle_it 2.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.81 r_dihedral_angle_4_deg 24.43 r_dihedral_angle_3_deg 14.998 r_long_range_B_refined 7.612 r_long_range_B_other 7.61 r_dihedral_angle_1_deg 5.637 r_scangle_other 4.523 r_scbond_it 2.887 r_scbond_other 2.872 r_mcangle_it 2.762 r_mcangle_other 2.76 r_mcbond_it 1.87 r_mcbond_other 1.866 r_angle_refined_deg 1.729 r_angle_other_deg 1.028 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 1386 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing