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DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Mycoplanecin A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 0.2 M CaCl2
0.15 M MgCl2
8.75 % (v/v) Glycerol
17.5 % (w/v) PEG 3350
0.1 M Tris/HCl pH 9.0
Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol.
Crystal Properties Matthews coefficient Solvent content 2.53 51.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.937 α = 90 b = 150.05 β = 103.92 c = 72.381 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 PIXEL DECTRIS EIGER2 X 16M 2022-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033202 PETRA III, DESY P11
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 2.27 75.03 99 0.115 0.124 0.046 0.995 6.8 7 39802
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 2.27 2.39 98.7 0.66 0.716 0.274 0.829 6.7
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 2.27 51.28 1.37 39787 1961 98.9 0.2089 0.2074 0.2072 0.2373 0.2371
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 7.254 f_angle_d 0.586 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5784 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement