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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 1MOJ PDB entry 1MOJ
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 MARRESEARCH 2003-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.731 SLS X06SA
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 2.9 15 94.2 0.093 9.75 3.8 15444 2 61.5
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 1MOJ 2.9 15 15444 1183 97.73 0.18396 0.17782 0.26281 RANDOM 58.447
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] -2.66 -1.33 -2.66 3.99
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.469 r_dihedral_angle_1_deg 7.941 r_scbond_it 6.265 r_angle_refined_deg 4.378 r_mcangle_it 3.169 r_mcbond_it 1.518 r_nbd_refined 0.321 r_symmetry_vdw_refined 0.294 r_chiral_restr 0.258 r_xyhbond_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 10.469 r_dihedral_angle_1_deg 7.941 r_scbond_it 6.265 r_angle_refined_deg 4.378 r_mcangle_it 3.169 r_mcbond_it 1.518 r_nbd_refined 0.321 r_symmetry_vdw_refined 0.294 r_chiral_restr 0.258 r_xyhbond_nbd_refined 0.209 r_symmetry_hbond_refined 0.171 r_metal_ion_refined 0.148 r_bond_refined_d 0.06 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5459 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing