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Getah virus macro domain in complex with ADPr, pose 1
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, 3mM ADPr, 3 hours soaking with crystallization solutution additioned 15mM Aspartic acid,
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.729 α = 90 b = 71.566 β = 90 c = 98.693 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 2.05 42.23 98.6 0.27 0.27 0.16 0.097 0.994 8.5 4.8 21125 25.5
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 2.05 2.11 99 1.206 1.206 1.517 0.908 0.468 1.5 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 6QZU 2.05 40.66 19838 1238 98.27 0.19514 0.19273 0.23548 0.2167 RANDOM 35.65
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] -2.64 -1.52 4.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 13.94 r_long_range_B_refined 6.533 r_long_range_B_other 6.481 r_dihedral_angle_1_deg 6.279 r_scangle_other 4.494 r_mcangle_it 3.246 r_mcangle_other 3.245 r_scbond_it 2.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 17.812 r_dihedral_angle_3_deg 13.94 r_long_range_B_refined 6.533 r_long_range_B_other 6.481 r_dihedral_angle_1_deg 6.279 r_scangle_other 4.494 r_mcangle_it 3.246 r_mcangle_other 3.245 r_scbond_it 2.777 r_scbond_other 2.775 r_mcbond_it 2.123 r_mcbond_other 2.117 r_angle_refined_deg 1.436 r_angle_other_deg 1.334 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 2386 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing