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Human DJ-1, 30 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography, CrystFEL processed
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Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished DJ-1 structure from X-ray source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 3.15 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.03 α = 90 b = 76.03 β = 90 c = 76.14 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 CCD RAYONIX MX340-HS 2022-11-12 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.240-1.016 APS 14-ID-B
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 concentric flow microfluidic mixer injection
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 1007 1051 1007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.77 65.84 98.98 0.98 0.1375 3.64 60.65 24993 27.93
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 1.77 1.8 98.7 0.04 58.4
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 2.01 32.96 1.34 17196 861 99.05 0.1631 0.162 0.1617 0.1832 0.181 34.35
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 13.6099 f_angle_d 0.6329 f_chiral_restr 0.0447 f_plane_restr 0.0035 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1400 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Precognition data reduction CrystFEL data scaling PHENIX phasing