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The X-ray structure of Ferritin from Pyrococcus furiosus loaded with Ag(I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JD6 PDB ENTRY 2JD6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2.1-2.3 M AMMONIUM SULFATE, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.4 63.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.681 α = 90 b = 157.681 β = 90 c = 246.437 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 RAYONIX M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 3.1 50 99 0.1 12 8.7 107788 -3 65.9
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 3.1 3.21 99 0.53 2 7.8
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 PDB ENTRY 2JD6 3.1 50 102347 5386 98.85 0.26132 0.26014 0.2483 0.28338 0.2692 RANDOM 73.616
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] 3.01 3.01 -6.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_3_deg 14.148 r_dihedral_angle_4_deg 10.58 r_dihedral_angle_1_deg 3.837 r_angle_refined_deg 0.744 r_scangle_it 0.466 r_scbond_it 0.362 r_mcangle_it 0.332 r_mcbond_it 0.178 r_chiral_restr 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_3_deg 14.148 r_dihedral_angle_4_deg 10.58 r_dihedral_angle_1_deg 3.837 r_angle_refined_deg 0.744 r_scangle_it 0.466 r_scbond_it 0.362 r_mcangle_it 0.332 r_mcbond_it 0.178 r_chiral_restr 0.044 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33983 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing