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Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Rickettsia rickettsii bound to griselimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 RiriA.17987.a.B1.PS38222 at 20 mg/mL with 2 mM griselimycin against Morpheus screen condition G12 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M NPS, 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 308710c12, unique puck ID zni8-8
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.21 α = 109.38 b = 82.79 β = 89.94 c = 82.86 γ = 106.53
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 MARMOSAIC 300 mm CCD 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 45.9 97.3 0.062 0.071 0.997 13.18 3.914 153460 35.829
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 91.4 0.348 0.412 0.906 3.29 3.547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6DLK 1.85 45.9 1.98 153419 1968 97.36 0.1692 0.1688 0.1694 0.2061 0.205 38.0808
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11710 Nucleic Acid Atoms Solvent Atoms 1301 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction