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Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PFC used directly in silico model SwissModel 5VFT used directly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.391 α = 90 b = 68.599 β = 92.78 c = 49.851 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 XE 16M 2021-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9796 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.17 68.6 100 0.118 0.122 0.033 0.999 10.9 13.8 15199
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.24 99.9 2.599 2.7 0.729 0.436 13.6
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 (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 2.17 49.84 14486 697 99.99 0.20035 0.19791 0.2065 0.25225 0.2614 RANDOM 59.824
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] -0.32 0.42 -1.29 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.891 r_dihedral_angle_3_deg 15.302 r_dihedral_angle_4_deg 13.347 r_dihedral_angle_1_deg 7.558 r_long_range_B_refined 4.398 r_long_range_B_other 4.396 r_scangle_other 2.427 r_mcangle_it 2.285 r_mcangle_other 2.285 r_scbond_it 1.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.891 r_dihedral_angle_3_deg 15.302 r_dihedral_angle_4_deg 13.347 r_dihedral_angle_1_deg 7.558 r_long_range_B_refined 4.398 r_long_range_B_other 4.396 r_scangle_other 2.427 r_mcangle_it 2.285 r_mcangle_other 2.285 r_scbond_it 1.512 r_scbond_other 1.512 r_mcbond_it 1.509 r_mcbond_other 1.509 r_angle_refined_deg 1.442 r_angle_other_deg 1.184 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 2200 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing