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Trans complex of phospho parkin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GLC
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,1.0 M 8.5 Tris (base), BICINE, 25% v/v MPD; 25% PEG 1000, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.804 α = 90 b = 83.804 β = 90 c = 105.033 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 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) 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 1.92 42.6 99.7 0.998 13.7 5.6 33029
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 1.92 1.97 0.724
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 6GLC 1.92 42.6 31316 1675 99.635 0.206 0.2048 0.2052 0.2325 0.2331 60.224
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] -0.904 -0.452 -0.904 2.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.933 r_dihedral_angle_3_deg 17.322 r_dihedral_angle_4_deg 15.914 r_lrange_it 7.159 r_dihedral_angle_1_deg 5.698 r_mcangle_it 5.05 r_scangle_it 4.996 r_scbond_it 3.821 r_mcbond_it 3.699 r_rigid_bond_restr 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.933 r_dihedral_angle_3_deg 17.322 r_dihedral_angle_4_deg 15.914 r_lrange_it 7.159 r_dihedral_angle_1_deg 5.698 r_mcangle_it 5.05 r_scangle_it 4.996 r_scbond_it 3.821 r_mcbond_it 3.699 r_rigid_bond_restr 0.839 r_angle_refined_deg 0.829 r_nbtor_refined 0.302 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.072 r_metal_ion_refined 0.029 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2911 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASES phasing