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An E. coli DPS protein from ferritin superfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 298 50 mM Sodium Acetate (pH: 5.9);
100 mM NaCl and
5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.625 α = 90 b = 133.969 β = 90 c = 139.112 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 PIXEL DECTRIS PILATUS3 6M 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9844 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.449 48.247 98.5 3.7 4.2 190268
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1f30 1.5 48.247 164388 8675 99.16 0.17796 0.17639 0.20767 0.2144 RANDOM 14.276
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] 0.4 -0.31 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 5.093 r_long_range_B_refined 4.827 r_long_range_B_other 4.827 r_scangle_other 3.57 r_scbond_it 2.411 r_scbond_other 2.407 r_mcangle_other 2.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.003 r_dihedral_angle_4_deg 17.97 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 5.093 r_long_range_B_refined 4.827 r_long_range_B_other 4.827 r_scangle_other 3.57 r_scbond_it 2.411 r_scbond_other 2.407 r_mcangle_other 2.061 r_mcangle_it 2.059 r_angle_refined_deg 2.018 r_mcbond_it 1.429 r_mcbond_other 1.429 r_angle_other_deg 1.124 r_chiral_restr 0.131 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7444 Nucleic Acid Atoms Solvent Atoms 1039 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement