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Crystal structure of E. coli YcbB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298.15 0.2 uL protein solution (30 mg/mL purified protein in 20 mM HEPES pH 8.0, 300 mM NaCl) and 1 uL of mother liquor (1.44 M lithium sulfate, 0.08 M HEPES pH 7.5, 0.02 M sodium acetate pH 4.6, 0.015 M ammonium sulfate, 4% (w/v) polyethylene glycol (PEG) 2000 monomethyl ether (MME)) with the addition of 1 mM meropenem and L-Ala-D-Glu-mDAP-D-Ala at 1 mM
Crystal Properties Matthews coefficient Solvent content 2.75 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.499 α = 90 b = 126.499 β = 90 c = 88.801 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 PIXEL DECTRIS PILATUS3 6M 2018-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.75 89.448 90.4 0.415 0.437 0.132 0.995 3.2 9.4 18943 65.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 33.6 1.4
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 THROUGHOUT 2.76 89.448 1.33 18943 953 99.31 0.2583 0.2561 0.2587 0.2981 0.3003
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 19.059 f_angle_d 1.878 f_chiral_restr 0.11 f_plane_restr 0.014 f_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3980 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing