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Getah virus macro domain in complex with ADPr, pose 2
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 6 293 Imidazole-Malate pH 6,0 30% PEG 4K, 3 mM ADPr, 50 mM Glutamic acid
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.88 α = 90 b = 71.647 β = 90 c = 98.803 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 1.7 42.35 97.5 0.055 0.055 0.069 0.04 0.999 15.6 5 36394 18.9
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 1.7 1.73 97.4 0.905 0.905 1.127 0.664 0.527 1.6 5.3
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 1.7 40.7 34198 2145 97.15 0.18258 0.18108 0.1917 0.20753 0.2179 RANDOM 26.139
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] -1.89 -0.74 2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.11 r_dihedral_angle_4_deg 16.697 r_dihedral_angle_3_deg 13.313 r_long_range_B_refined 6.425 r_long_range_B_other 6.425 r_dihedral_angle_1_deg 5.907 r_scangle_other 4.875 r_scbond_it 3.327 r_scbond_other 3.326 r_mcangle_it 2.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.11 r_dihedral_angle_4_deg 16.697 r_dihedral_angle_3_deg 13.313 r_long_range_B_refined 6.425 r_long_range_B_other 6.425 r_dihedral_angle_1_deg 5.907 r_scangle_other 4.875 r_scbond_it 3.327 r_scbond_other 3.326 r_mcangle_it 2.989 r_mcangle_other 2.989 r_mcbond_it 2.211 r_mcbond_other 2.196 r_angle_other_deg 1.319 r_angle_refined_deg 1.25 r_chiral_restr 0.057 r_bond_refined_d 0.005 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 231 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing