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Human DJ-1, 15 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished room temperature DJ-1 X-ray crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293 100 mM HEPES pH=7.5, 200 mM NaCl, and 15% 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 2022-11-13 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 injector injection
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 1050 1864 1050
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 flow-focused diffusive mixer 1 (µl/min) undefined (µm)
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 1.77 65.84 99.86 0.99 20.43 65 25225 -0.23
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 1.83 99.88 0.35 2.39 22
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 1.77 65.84 1.74 25193 1145 99.87 0.2017 0.2003 0.2015 0.2307 0.2325 14.94
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 14.1752 f_angle_d 1.6772 f_chiral_restr 0.0766 f_bond_d 0.0161 f_plane_restr 0.0115
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 careless data scaling PHENIX phasing