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Human DJ-1, 6.5-18.5 min mixing with methylglyoxal, fixed target serial crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished DJ-1 structure from X-ray source
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293 100 mM HEPES, 200 mM NaCl, 15% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.234 α = 90 b = 76.234 β = 90 c = 76.392 γ = 120
Symmetry Space Group P 31 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 293 PIXEL DECTRIS EIGER2 X 16M 2024-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.969 CHESS 7B2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Microcrystals raster scanned on a grid
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 1.69 66.02 99.31 0.295 0.976 6.6 12.8 28986 25.75
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 1.69 1.72 99.86 5.56 0.066
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.69 49.95 1.33 28909 1931 99.05 0.1584 0.1572 0.1575 0.1751 0.1748 32.57
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 13.4955 f_angle_d 0.7786 f_chiral_restr 0.0546 f_bond_d 0.0074 f_plane_restr 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1383 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHENIX phasing