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X-ray structure of Auranofin-horse spleen ferritin
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 7.2 293 0.8 M ammonium sulphate
0.1 M TrisHCl pH 7.4
60 mM cadmium sulphate
Crystal Properties Matthews coefficient Solvent content 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.99 α = 90 b = 181.99 β = 90 c = 181.99 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 PILATUS 6M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.24 64.34 100 0.122 0.014 1 34.9 20 88885
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 1.24 1.26 100 1.8 0.364 0.772 15
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ERK 1.24 64.34 88885 4449 98.147 0.159 0.1582 0.1671 0.1798 0.1908 15.916
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 34.164 r_dihedral_angle_4_deg 19.022 r_dihedral_angle_3_deg 12.671 r_lrange_it 7.885 r_lrange_other 7.275 r_dihedral_angle_1_deg 5.32 r_scangle_other 4.681 r_scangle_it 4.672 r_scbond_it 3.106 r_scbond_other 3.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.164 r_dihedral_angle_4_deg 19.022 r_dihedral_angle_3_deg 12.671 r_lrange_it 7.885 r_lrange_other 7.275 r_dihedral_angle_1_deg 5.32 r_scangle_other 4.681 r_scangle_it 4.672 r_scbond_it 3.106 r_scbond_other 3.095 r_mcangle_it 2.37 r_mcangle_other 2.369 r_angle_refined_deg 2.243 r_mcbond_it 1.899 r_mcbond_other 1.801 r_angle_other_deg 1.66 r_symmetry_nbd_refined 0.341 r_symmetry_xyhbond_nbd_refined 0.325 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.271 r_nbd_other 0.246 r_symmetry_nbd_other 0.202 r_ext_dist_refined_d 0.198 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_other 0.145 r_chiral_restr 0.119 r_symmetry_nbtor_other 0.092 r_metal_ion_refined 0.091 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1370 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing