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Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DPS Dps-protein from E. coli - PDB entry 1DPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG400, 1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.11 α = 90 b = 91.11 β = 90 c = 150.04 γ = 120
Symmetry Space Group P 3 2 1
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 4 2003-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.93 ESRF ID29
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 1.6 158 96.5 0.074 10 5.5 92251 2 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.641 99.1
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Dps-protein from E. coli - PDB entry 1DPS 1.6 15 87268 6766 98.53 0.16808 0.16484 0.21039 RANDOM 21.515
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] -0.33 -0.17 -0.33 0.5
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.308 r_dihedral_angle_1_deg 4.862 r_scbond_it 3.806 r_mcangle_it 1.895 r_angle_refined_deg 1.509 r_mcbond_it 0.952 r_angle_other_deg 0.934 r_symmetry_vdw_other 0.306 r_symmetry_hbond_refined 0.269 r_xyhbond_nbd_refined 0.265
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.308 r_dihedral_angle_1_deg 4.862 r_scbond_it 3.806 r_mcangle_it 1.895 r_angle_refined_deg 1.509 r_mcbond_it 0.952 r_angle_other_deg 0.934 r_symmetry_vdw_other 0.306 r_symmetry_hbond_refined 0.269 r_xyhbond_nbd_refined 0.265 r_nbd_other 0.26 r_nbd_refined 0.255 r_symmetry_vdw_refined 0.202 r_chiral_restr 0.125 r_nbtor_other 0.09 r_metal_ion_refined 0.044 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5459 Nucleic Acid Atoms Solvent Atoms 796 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing