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pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.16 43.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.45 α = 90 b = 76.426 β = 100.485 c = 114.329 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 EIGER X 4M 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 38.39 96.5 0.995 7.7 3.1 31088
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 2.35 2.43 0.686
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 5CAW 2.35 38.242 29561 1512 96.318 0.199 0.1981 0.199 0.2169 0.2165 44.93
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] 1.223 -0.211 1.811 -2.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.745 r_dihedral_angle_3_deg 16.574 r_dihedral_angle_4_deg 15.546 r_lrange_it 6.42 r_dihedral_angle_1_deg 6.319 r_scangle_it 3.243 r_mcangle_it 3.189 r_scbond_it 1.931 r_mcbond_it 1.8 r_angle_refined_deg 0.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.745 r_dihedral_angle_3_deg 16.574 r_dihedral_angle_4_deg 15.546 r_lrange_it 6.42 r_dihedral_angle_1_deg 6.319 r_scangle_it 3.243 r_mcangle_it 3.189 r_scbond_it 1.931 r_mcbond_it 1.8 r_angle_refined_deg 0.836 r_nbtor_refined 0.302 r_symmetry_nbd_refined 0.243 r_nbd_refined 0.186 r_metal_ion_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.143 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.075 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6029 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing