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Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby) complexed with Met-1 linked di-ubiquitin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 100 mM Tris-HCl, pH 8.5, 200 mM magnesium chloride and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.74 α = 90 b = 102.09 β = 90 c = 90.92 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2017-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97736 SSRF BL18U1
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 2.05 50.01 100 0.056 0.061 0.999 17.67 6.975 87704 52.129
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 2.05 2.17 100 0.568 0.613 0.934 3.6 7.033
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 SAD THROUGHOUT 2.05 50.01 43764 2331 99.98 0.2142 0.2124 0.2458 0.2678 RANDOM 60.34
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] 4.17 -2.71 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 15.18 r_dihedral_angle_1_deg 6.17 r_angle_refined_deg 1.388 r_angle_other_deg 0.894 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.946 r_dihedral_angle_4_deg 15.813 r_dihedral_angle_3_deg 15.18 r_dihedral_angle_1_deg 6.17 r_angle_refined_deg 1.388 r_angle_other_deg 0.894 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5234 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing