☰ Navigation Tabs
Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.54 68.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.352 α = 90 b = 151.352 β = 90 c = 183.778 γ = 90
Symmetry Space Group P 43 21 2
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 2019-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
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 2.35 92.48 99.8 0.078 0.083 0.03 0.999 17.4 7.4 89409 42.7
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 2.35 2.39 1.07 1.147 0.403 0.791 2.5
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 FREE R-VALUE 2A6Q 2.35 53.51 1.34 89296 4531 99.78 0.1985 0.1971 0.2003 0.2225 0.2264 57.54
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 25.5523 f_angle_d 0.6581 f_chiral_restr 0.0424 f_bond_d 0.0037 f_plane_restr 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7305 Nucleic Acid Atoms 1855 Solvent Atoms 315 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing