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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 1TJO PDB entry 1TJO
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 2003-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.731 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 2.2 158.11 98.7 0.11 11.11 6 36571 2 37.7
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 PDB entry 1TJO 2.2 158.11 34298 2629 99.72 0.17651 0.1721 0.23543 RANDOM 31.19
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] -0.36 -0.18 -0.36 0.54
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.148 r_dihedral_angle_1_deg 5.815 r_scbond_it 5.028 r_mcangle_it 2.364 r_angle_refined_deg 2.254 r_angle_other_deg 1.229 r_mcbond_it 1.17 r_symmetry_vdw_refined 0.344 r_symmetry_vdw_other 0.336 r_nbd_other 0.268
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.148 r_dihedral_angle_1_deg 5.815 r_scbond_it 5.028 r_mcangle_it 2.364 r_angle_refined_deg 2.254 r_angle_other_deg 1.229 r_mcbond_it 1.17 r_symmetry_vdw_refined 0.344 r_symmetry_vdw_other 0.336 r_nbd_other 0.268 r_nbd_refined 0.251 r_symmetry_hbond_refined 0.239 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.17 r_nbtor_other 0.143 r_metal_ion_refined 0.086 r_bond_refined_d 0.033 r_gen_planes_other 0.03 r_gen_planes_refined 0.02 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5459 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling MOLREP phasing