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X-ray structure of human heavy chain ferritin in complex with cisplatin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0 M Magnesium chloride, 0.1 M bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.03 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.069 α = 90 b = 183.069 β = 90 c = 183.069 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 2006-09-15 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) 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 2.05 105.7 98.5 0.143 0.053 17.8 7.9 16819
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 91.8 0.588 0.236 0.837 3.7 6.9
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 4Y08 2.05 105.69 15963 837 98.41 0.1646 0.1625 0.1744 0.2057 0.2211 RANDOM 19.358
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 39.801 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.955 r_long_range_B_refined 7.487 r_long_range_B_other 6.933 r_dihedral_angle_1_deg 5.826 r_scangle_other 4.552 r_scbond_it 3.693 r_scbond_other 3.411 r_mcangle_other 3.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.801 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 12.955 r_long_range_B_refined 7.487 r_long_range_B_other 6.933 r_dihedral_angle_1_deg 5.826 r_scangle_other 4.552 r_scbond_it 3.693 r_scbond_other 3.411 r_mcangle_other 3.072 r_mcangle_it 3.071 r_angle_refined_deg 1.919 r_mcbond_it 1.842 r_mcbond_other 1.812 r_angle_other_deg 1.007 r_chiral_restr 0.103 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 1424 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing