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Crystal structure of a DNA polymerase III subunit beta DnaN sliding clamp from Rickettsia typhi str. Wilmington
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 287 24.49 mg/mL RityA.17987.a.B1.PW38354 against JCSG+ screen condition C6 = 0.1 M phosphate/citrate pH 4.2, 40% PEG 300, direct cryo, 295697c6, ffq4-2
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.52 α = 90 b = 43.05 β = 121.39 c = 83.17 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 300 mm CCD 2018-04-05 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 2 41.533 98.7 0.049 0.056 0.999 16 4.118 30248 33.98
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 2 2.05 98.4 0.489 0.559 0.937 3.52 4.228
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 5w7z 2 41.533 1.37 30232 1969 98.93 0.1771 0.1743 0.1766 0.2166 0.217 47.633
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 2836 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 27
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction