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Crystal structure of the cytosolic domain of Tribolium castaneum PINK1 in the non-phosphorylated state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1M HEPES (pH 7.0), 0.15M (NH4)2 SO4, 20% PEG 4K. Temp = 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.914 α = 90 b = 52.914 β = 90 c = 545.362 γ = 120
Symmetry Space Group P 61 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 PILATUS3 S 6M 2020-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 49.58 100 0.737 0.989 6.1 16.4 10223 62.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 100 3.613 0.627 1.1 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5YJ9 3 45.82 1.34 10223 478 99.81 0.2564 0.2538 0.3062 0.2542 72.81
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.2406 f_angle_d 0.6679 f_chiral_restr 0.0412 f_plane_restr 0.007 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3014 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling PHENIX phasing