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Ternary trans-complex of phospho-parkin with cis ACT and pUb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8IKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate, Imidazole, MES monohydrate (acid), 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.764 α = 90 b = 82.764 β = 90 c = 103.494 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2023-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.9795 ESRF BM07
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 38.42 99.9 0.144 0.998 17.1 13.1 13050
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 0.791
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8IKM 2.6 38.42 12333 691 99.87 0.214 0.2125 0.2088 0.2358 0.2341 63.575
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] -1.814 -0.907 -1.814 5.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 9.993 r_dihedral_angle_1_deg 5.887 r_lrange_it 5.687 r_mcangle_it 2.945 r_scangle_it 2.729 r_scbond_it 1.841 r_mcbond_it 1.836 r_angle_refined_deg 0.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.857 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 9.993 r_dihedral_angle_1_deg 5.887 r_lrange_it 5.687 r_mcangle_it 2.945 r_scangle_it 2.729 r_scbond_it 1.841 r_mcbond_it 1.836 r_angle_refined_deg 0.844 r_nbtor_refined 0.303 r_rigid_bond_restr 0.237 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.188 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2977 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing