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Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MFR Bullfrog M ferritin, PDB ENTRY 1MFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 15% PEG 1000, 0.2M calcium acetate, 0.1M imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.61 α = 90 b = 220.886 β = 90 c = 122.452 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD Bruker DIP-6040 2009-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 98.9 0.058 18.4 5.8 552676 546597 1 13.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.83 97.1 0.259 7.96 4.6 26571
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT Bullfrog M ferritin, PDB ENTRY 1MFR 1.8 49.468 1.34 553039 546458 27445 98.81 0.1439 0.1423 0.1589 0.1727 0.1851 RANDOM 20.99
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] 5.5668 -2.4738 -3.0929
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.883 f_angle_d 0.771 f_chiral_restr 0.054 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39263 Nucleic Acid Atoms Solvent Atoms 4568 Heterogen Atoms 208
Software Software Software Name Purpose HKL-2000 data collection CNS refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing