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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, 1 M 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 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 97.6 0.079 8.99 11 34572 2 18.9
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 2.2 141.42 34572 1823 99.79 0.18792 0.18526 0.23758 RANDOM 46.409
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] -1.1 -0.55 -1.1 1.65
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.615 r_dihedral_angle_1_deg 6.294 r_scbond_it 4.852 r_angle_refined_deg 2.506 r_mcangle_it 2.18 r_mcbond_it 1.169 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.222 r_symmetry_hbond_refined 0.209 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.615 r_dihedral_angle_1_deg 6.294 r_scbond_it 4.852 r_angle_refined_deg 2.506 r_mcangle_it 2.18 r_mcbond_it 1.169 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.222 r_symmetry_hbond_refined 0.209 r_chiral_restr 0.187 r_xyhbond_nbd_refined 0.175 r_metal_ion_refined 0.075 r_bond_refined_d 0.034 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5459 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling MOLREP phasing