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Human heavy chain ferritin with introduced Cys residues modified with C10 ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JKK 5JKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Crystallization of little amounts of protein or functionalized protein variants were performed via hanging drop vapor diffusion techniques. Reservoir solution (100 mM Tris, 500 mM MgOAc, pH 8.5) was prepared in a 24- well manual plate set. Drops were prepared on siliconized glass cover slides (Jena Bioscience) by mixing 2 microL reservoir solutions with 1 microL 50 mM Tris, 1 M NaCl, pH 7.5 buffer and 1 microL of respective ferritin variant. Plates were incubated at 298K. After one day first crystals were visible.
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.44 α = 90 b = 181.44 β = 90 c = 181.44 γ = 90
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 EIGER R 4M 2021-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 2 48.54 99.9 0.052 0.054 0.012 1 43.2 20.9 132696
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 2 2.03 98.5 0.181 0.186 0.041 0.995 20.2
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 5JKK 2 48.54 131264 2101 99.86 0.1449 0.1444 0.158 0.177 0.1889 RANDOM 16.458
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 38.293 r_dihedral_angle_4_deg 20.865 r_dihedral_angle_3_deg 11.787 r_dihedral_angle_1_deg 5.311 r_angle_refined_deg 1.675 r_angle_other_deg 1.508 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.293 r_dihedral_angle_4_deg 20.865 r_dihedral_angle_3_deg 11.787 r_dihedral_angle_1_deg 5.311 r_angle_refined_deg 1.675 r_angle_other_deg 1.508 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11301 Nucleic Acid Atoms Solvent Atoms 1076 Heterogen Atoms 135
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing