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Crystal structure of iron bound Dps protein (PA0962) from Pseudomonas aeruginosa (cubic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 8% (w/v) PEG 8000, 100 mM Hepes. Soaking: crystals were transferred to a solution containing 80% crystallant, 20% PEG 200 and 50 mM FeCl2 and soaked for 10 minutes. Samples were harvested directly from the soaking solution
Crystal Properties Matthews coefficient Solvent content 3.34 63.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.9 α = 90 b = 223.9 β = 90 c = 223.9 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 PIXEL DECTRIS EIGER2 XE 9M 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.85 48.86 100 0.149 0.153 0.034 0.999 15.2 20.8 315151
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 1.985 2.035 0.444 0.684 21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 43.91 1.01 314959 15615 99.96 0.1633 0.1618 0.171 0.1919 0.1985
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.035 f_angle_d 0.989 f_chiral_restr 0.051 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19267 Nucleic Acid Atoms Solvent Atoms 2111 Heterogen Atoms 135
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing