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X-ray structure of Auranofin-human H-chain ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0 M magnesium chloride
0.1 M Bicine buffer pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.07 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.03 α = 90 b = 184.03 β = 90 c = 184.03 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 12M 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) 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 1.17 46.05 100 0.156 0.157 0.018 1 26.6 20 90295
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.19 100 1.8 1 0.378 0.777 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 FREE R-VALUE 5N27 1.17 46.05 89608 4431 99.967 0.15 0.149 0.1489 0.1665 0.1661 13.745
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 39.63 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 12.484 r_lrange_it 6.813 r_dihedral_angle_1_deg 5.749 r_lrange_other 5.731 r_scangle_it 4.017 r_scangle_other 3.99 r_scbond_it 2.613 r_scbond_other 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.63 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 12.484 r_lrange_it 6.813 r_dihedral_angle_1_deg 5.749 r_lrange_other 5.731 r_scangle_it 4.017 r_scangle_other 3.99 r_scbond_it 2.613 r_scbond_other 2.611 r_angle_refined_deg 2.196 r_mcangle_it 2.015 r_mcangle_other 1.999 r_angle_other_deg 1.657 r_mcbond_it 1.328 r_mcbond_other 1.308 r_symmetry_xyhbond_nbd_refined 0.35 r_nbd_refined 0.315 r_symmetry_nbd_refined 0.279 r_xyhbond_nbd_refined 0.27 r_nbd_other 0.21 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.19 r_chiral_restr 0.12 r_ext_dist_refined_d 0.118 r_symmetry_nbtor_other 0.091 r_metal_ion_refined 0.061 r_symmetry_metal_ion_refined 0.027 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1423 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing