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Revelation of Endogenously bound Fe2+ ions in the Crystal Structure of Ferritin from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 10mM Mg hexahydrtae, 2.0M Lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.02 59.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.998 α = 90 b = 127.998 β = 90 c = 170.902 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 CCD ADSC QUANTUM 315 Si III 2012-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.00 SPring-8 BL26B2
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 2.5 50 100 0.092 13.9 3.9 45052 2 2
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 2.5 2.54 100 0.566 1.6 3.7 4667
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-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 1EUM 2.5 50 45052 2402 99.96 0.17506 0.17506 0.17188 0.1744 0.23539 0.237 RANDOM 47.757
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.219 r_dihedral_angle_4_deg 21.564 r_dihedral_angle_3_deg 18.503 r_long_range_B_refined 9.792 r_long_range_B_other 9.789 r_scangle_other 6.581 r_mcangle_other 5.761 r_mcangle_it 5.76 r_dihedral_angle_1_deg 5.638 r_scbond_it 4.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.219 r_dihedral_angle_4_deg 21.564 r_dihedral_angle_3_deg 18.503 r_long_range_B_refined 9.792 r_long_range_B_other 9.789 r_scangle_other 6.581 r_mcangle_other 5.761 r_mcangle_it 5.76 r_dihedral_angle_1_deg 5.638 r_scbond_it 4.248 r_scbond_other 4.248 r_mcbond_it 3.68 r_mcbond_other 3.675 r_angle_refined_deg 1.523 r_angle_other_deg 0.836 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8148 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 149
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction SCALA data scaling CCP4 phasing