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DupA from legionella covalently bound to ubiquitin-based probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 20% PEG 6000
0.1 M HEPES pH7
0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.21 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.808 α = 90 b = 86.808 β = 90 c = 146.539 γ = 120
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 2M 2022-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.17 75.3 100 0.043 0.998 10.7 5 65360
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.22 100 0.763 0.388 0.9 4.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.17 75.291 65309 3239 99.988 0.188 0.185 0.1902 0.2389 0.2488 65.654
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] -0.174 -0.087 -0.174 0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.51 r_dihedral_angle_6_deg 15.008 r_dihedral_angle_2_deg 10.822 r_lrange_other 7.979 r_lrange_it 7.976 r_dihedral_angle_1_deg 7.411 r_scangle_it 5.447 r_scangle_other 5.447 r_mcangle_it 3.952 r_mcangle_other 3.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.51 r_dihedral_angle_6_deg 15.008 r_dihedral_angle_2_deg 10.822 r_lrange_other 7.979 r_lrange_it 7.976 r_dihedral_angle_1_deg 7.411 r_scangle_it 5.447 r_scangle_other 5.447 r_mcangle_it 3.952 r_mcangle_other 3.951 r_scbond_it 3.846 r_scbond_other 3.846 r_mcbond_it 2.711 r_mcbond_other 2.71 r_angle_refined_deg 1.835 r_angle_other_deg 0.653 r_symmetry_nbd_refined 0.264 r_nbd_other 0.261 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.223 r_chiral_restr 0.208 r_symmetry_nbd_other 0.201 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9221 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing