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Crystal structure of Ag+ binding to Dendrorhynchus zhejiangensis ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291.15 DzFer crystals were grown in 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v PEG monomethyl ether 2000, followed by soaking for 10 min with 20% glycerol and 100 mM AgNO3.
Crystal Properties Matthews coefficient Solvent content 3.65 66.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.212 α = 90 b = 148.212 β = 90 c = 148.212 γ = 90
Symmetry Space Group I 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 EIGER2 X 9M 2022-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL17B 0.979 NFPSS BL17B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 106.78 99.7 0.99 7.2 11.3 21003
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 1.9 2 0.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 104.8 21003 1107 99.95 0.15273 0.1508 0.18965 0.2113 RANDOM 35.17
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 38.613 r_dihedral_angle_4_deg 16.748 r_dihedral_angle_3_deg 14.023 r_long_range_B_refined 8.426 r_long_range_B_other 8.348 r_scangle_other 7.539 r_dihedral_angle_1_deg 5.302 r_scbond_it 5.209 r_scbond_other 5.169 r_mcangle_other 3.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.613 r_dihedral_angle_4_deg 16.748 r_dihedral_angle_3_deg 14.023 r_long_range_B_refined 8.426 r_long_range_B_other 8.348 r_scangle_other 7.539 r_dihedral_angle_1_deg 5.302 r_scbond_it 5.209 r_scbond_other 5.169 r_mcangle_other 3.925 r_mcangle_it 3.913 r_mcbond_it 2.904 r_mcbond_other 2.822 r_angle_refined_deg 1.875 r_angle_other_deg 1.098 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 1366 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction autoPROC data scaling BALBES phasing