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Crystal structure of Staphylococcus aureus DinG protein in complex with ssDNA and Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 5% v/v Tacsimate (pH 7.0), 0.1 M HEPES (pH 7.0), 8% w/v Polyethylene glycol monomethyl ether 5,000 and 50 mM CaCl2.
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.855 α = 90 b = 128.045 β = 90 c = 302.999 γ = 90
Symmetry Space Group C 2 2 21
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 315r 2022-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3.21 39.65 99.58 0.102 2.43 6 22275 111.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.21 3.33 1.514 2.7
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 3.21 39.65 1.34 22275 1106 99.58 0.2836 0.2833 0.2823 0.2917 0.2878 154.64
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 11.7352 f_angle_d 1.1548 f_chiral_restr 0.087 f_plane_restr 0.0124 f_bond_d 0.0081
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7280 Nucleic Acid Atoms 216 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing Coot model building