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Crystal structure of Cu2+ 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 291.15 0.2 M sodium citrate tribasic dihydrate, 0.1 M Tris hydrochloride pH 8.5, 30% v/v polyethyene glycol 400
Crystal Properties Matthews coefficient Solvent content 3.68 66.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.011 α = 90 b = 151.011 β = 90 c = 151.011 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 PILATUS3 S 6M 2019-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.979 NFPSS BL18U
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 1.38 106.9 80.66 0.065 0.069 0.022 0.997 5.3 7.6 13361 36.35
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 1.38 2.97 0.999
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.26 106.78 13361 667 99.86 0.16689 0.16406 0.1768 0.22639 0.2292 RANDOM 32.186
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 37.457 r_dihedral_angle_4_deg 17.763 r_dihedral_angle_3_deg 16.001 r_long_range_B_refined 7.882 r_long_range_B_other 7.837 r_scangle_other 6.538 r_dihedral_angle_1_deg 5.802 r_scbond_it 4.338 r_scbond_other 4.321 r_mcangle_other 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.457 r_dihedral_angle_4_deg 17.763 r_dihedral_angle_3_deg 16.001 r_long_range_B_refined 7.882 r_long_range_B_other 7.837 r_scangle_other 6.538 r_dihedral_angle_1_deg 5.802 r_scbond_it 4.338 r_scbond_other 4.321 r_mcangle_other 4.03 r_mcangle_it 4.027 r_mcbond_it 2.81 r_mcbond_other 2.792 r_angle_refined_deg 1.779 r_angle_other_deg 1.024 r_chiral_restr 0.109 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 155 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling BALBES phasing