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Getah virus macro domain in complex with ADPr in open conformation
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, 34% PEG 4K, 3 mM ADPr, 30mM Aspartic acid
Crystal Properties Matthews coefficient Solvent content 2.28 45.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.673 α = 90 b = 71.441 β = 90 c = 98.97 γ = 90
Symmetry Space Group P 21 21 21
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 4M 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 1.85 40.68 99.6 0.071 0.071 0.087 0.051 0.998 13.1 4.8 28867 18.4
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 1.85 1.89 99.8 1.107 1.107 1.369 0.792 0.627 1.4 5.1
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 FOURIER SYNTHESIS THROUGHOUT 6QZU 1.85 33.98 27122 1696 99.37 0.17017 0.16844 0.183 0.19901 0.2154 RANDOM 43.258
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] -2.42 -0.92 3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.656 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_3_deg 13.094 r_long_range_B_refined 7.15 r_long_range_B_other 7.067 r_dihedral_angle_1_deg 6.293 r_scangle_other 5.396 r_scbond_it 3.576 r_scbond_other 3.575 r_mcangle_it 3.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.656 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_3_deg 13.094 r_long_range_B_refined 7.15 r_long_range_B_other 7.067 r_dihedral_angle_1_deg 6.293 r_scangle_other 5.396 r_scbond_it 3.576 r_scbond_other 3.575 r_mcangle_it 3.311 r_mcangle_other 3.31 r_mcbond_it 2.455 r_mcbond_other 2.427 r_angle_refined_deg 1.454 r_angle_other_deg 1.363 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 2388 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing