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Getah virus macro domain in complex with ADPr covalently bond to Cys34
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.9 293 Imidazole-Malate pH 5.9, 38% PEG 4K, 3 mM ADPr, 3 mM Aspartic acid
Crystal Properties Matthews coefficient Solvent content 2.14 42.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.011 α = 90 b = 46.801 β = 104.16 c = 51.004 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 9M 2017-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98005 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.45 37.37 99.9 0.043 0.043 0.051 0.027 0.999 20.6 6.6 26026 17.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 100 0.749 0.749 0.895 0.484 0.775 2.1 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6QZU 1.45 37.37 24542 1483 99.86 0.17101 0.16946 0.1707 0.19667 0.1956 RANDOM 19.46
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] -0.67 -0.07 0.32 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 20.463 r_dihedral_angle_3_deg 10.896 r_scangle_other 9.451 r_long_range_B_refined 9.419 r_long_range_B_other 9.416 r_scbond_it 9.051 r_scbond_other 9.046 r_dihedral_angle_1_deg 5.983 r_mcangle_other 3.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.148 r_dihedral_angle_4_deg 20.463 r_dihedral_angle_3_deg 10.896 r_scangle_other 9.451 r_long_range_B_refined 9.419 r_long_range_B_other 9.416 r_scbond_it 9.051 r_scbond_other 9.046 r_dihedral_angle_1_deg 5.983 r_mcangle_other 3.516 r_mcangle_it 3.462 r_mcbond_it 3.301 r_mcbond_other 2.881 r_angle_refined_deg 1.583 r_angle_other_deg 1.551 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 1210 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing