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pUbl depleted Parkin complex with pUbiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
Crystal Properties Matthews coefficient Solvent content 3.98 69.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.805 α = 90 b = 187.805 β = 90 c = 141.857 γ = 120
Symmetry Space Group P 64 2 2
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 2022-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 3.3 39.15 92.85 0.1928 0.997 8.4 7.1 20948
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 3.3 3.56 0.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5N2W 3.3 39.15 19853 92.01 0.236 0.23415 0.26985 0.2447
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] 2.932 1.466 2.932 -9.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.811 r_dihedral_angle_3_deg 20.403 r_dihedral_angle_4_deg 17.265 r_lrange_it 13.673 r_scangle_it 9.129 r_mcangle_it 8.484 r_scbond_it 5.968 r_dihedral_angle_1_deg 5.591 r_mcbond_it 5.123 r_angle_refined_deg 1.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.811 r_dihedral_angle_3_deg 20.403 r_dihedral_angle_4_deg 17.265 r_lrange_it 13.673 r_scangle_it 9.129 r_mcangle_it 8.484 r_scbond_it 5.968 r_dihedral_angle_1_deg 5.591 r_mcbond_it 5.123 r_angle_refined_deg 1.061 r_nbtor_refined 0.303 r_symmetry_nbd_refined 0.286 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5457 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing