Navigation Tabs RT XFEL structure of Soybean Lipoxygenase-1 in large unit-cell
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.5 291 In a 2 mL Eppendorf Tube, 0.5 mL of precipitant (0.4M NaOAc pH=5.5, 16% PEG-3350) and 0.5 mL of SLO (10 mg/mL in 50 mM NaOAc, pH=5.0) was combined together with ~10uL of seed stock (see 2.2.1.) being added to the tube cap prior to mixing by inversion. The tube was then placed on a Thermo Fisher Tuber Revolver Rotator, set to 30 RPM. Samples were left to mix overnight. Subsequently, samples were mixed in a ~1:1 ratio with 18% hydroxyethylcellulose (Sigma-Aldrich PN-09368) dissolved in SLO precipitant (0.4M NaOAc pH=5.5, 16% PEG-3350)
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.031 α = 90 b = 94.536 β = 91.181 c = 50.529 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 CCD RAYONIX MX340-HS 2022-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE MFX 1.31 SLAC LCLS MFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 9% HEC injected via LCP style injector injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 30 (fs) 30 75 9.5 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 LCP-style injector undefined (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 1.95 19.59 98.9 0.989 0.109 4.416 77.59 65618 37.02
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 1.95 1.98 99.78 0.567 0.618 12.19
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.95 19.59 1.37 65618 2012 99.93 0.2131 0.2124 0.2124 0.2348 0.2346 65.8
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 11.9621 f_angle_d 0.5423 f_chiral_restr 0.0408 f_plane_restr 0.0056 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6258 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement cctbx.xfel data reduction cctbx.xfel.merge data scaling PHENIX phasing
