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XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2Y 3v2y, 4eiy experimental model PDB 4EIY 3v2y, 4eiy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7 295 crystallization in syringes in precipitant conditions containing 100-300 mM KH2PO4 monobasic, 28-32% v/v PEG400, and 100 mM HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 3.28 62.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.84 α = 90 b = 103.42 β = 90 c = 187.9 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 296 CCD RAYONIX MX225-HS 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER PAL-XFEL BEAMLINE NCI 1.278 PAL-XFEL NCI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 LCP injector injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 25 (fs) 30 6 9700 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 6918 6918 6918
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 LCP injector 0.15 (µl/min) undefined (µm)
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 2.2 30 99.93 0.92 0.244 3.8 119.3 60071 30.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.154 0.718 1.5 112
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3v2y, 4eiy 2.2 29.97 1.35 60071 1999 99.99 0.3017 0.3007 0.3096 0.3292 0.3358 48.9206
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5581 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 414
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing