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Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100 mM Na Cacodylate pH 7.0, 21% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.677 α = 90 b = 58.768 β = 114.42 c = 75.111 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2017-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9789 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 68.39 100 19.28 6.413 43941
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.85 68.39 41718 2208 99.67 0.16119 0.15908 0.20077 0.2052 RANDOM 31.956
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] -0.35 0.39 -0.37 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 14.353 r_long_range_B_refined 6.065 r_long_range_B_other 6.017 r_dihedral_angle_1_deg 5.998 r_scangle_other 3.934 r_scbond_it 2.569 r_scbond_other 2.568 r_mcangle_it 2.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 14.353 r_long_range_B_refined 6.065 r_long_range_B_other 6.017 r_dihedral_angle_1_deg 5.998 r_scangle_other 3.934 r_scbond_it 2.569 r_scbond_other 2.568 r_mcangle_it 2.266 r_mcangle_other 2.266 r_angle_refined_deg 1.965 r_mcbond_it 1.582 r_mcbond_other 1.581 r_angle_other_deg 0.928 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3685 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing