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Crystal structures of a novel open pore ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S3Q PDB entry 1S3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 7.5 293 PEG 400, HEPES, MgCl2, FeSO4 , pH 7.5, MICROBATCH UNDER OIL, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.502 α = 90 b = 190.243 β = 90 c = 179.407 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV osmic mirror 2003-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5418
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 2.7 80 99.9 0.097 26.43 86172 86172
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 0.394 0.394 6.67 8527
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1S3Q 2.7 30 86172 81803 4330 99.81 0.17877 0.17877 0.17672 0.185 0.21755 0.2208 RANDOM 19.829
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] -1.09 0.43 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.167 r_scangle_it 3.321 r_mcangle_it 2.734 r_scbond_it 2.088 r_mcbond_it 1.666 r_angle_refined_deg 1.461 r_angle_other_deg 1.135 r_symmetry_hbond_refined 0.471 r_nbd_other 0.279 r_xyhbond_nbd_refined 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.167 r_scangle_it 3.321 r_mcangle_it 2.734 r_scbond_it 2.088 r_mcbond_it 1.666 r_angle_refined_deg 1.461 r_angle_other_deg 1.135 r_symmetry_hbond_refined 0.471 r_nbd_other 0.279 r_xyhbond_nbd_refined 0.278 r_nbd_refined 0.267 r_symmetry_vdw_other 0.265 r_symmetry_vdw_refined 0.222 r_metal_ion_refined 0.12 r_nbtor_other 0.088 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16113 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling