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Room temperature structure of Glycine max phyA in Pfr/Pr ensemble
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8.5 296 0.1 M Tris (base), BICINE pH 8.5, 18% v/v PEG 500MME 9% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.83 56.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.45 α = 90 b = 115.05 β = 92.68 c = 69.8 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 293 PIXEL AGIPD 2023-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.33 European XFEL SPB/SFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 GVDN injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 20 (µl/min) undefined (µm) Shimadzu HPLC pumps LC-20AD) using 100 micrometer inner diameter tubing Crystal slurry, filtered
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 20.79 100 0.991 0.1088 7.88 1282.2 45135 47.56
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 0.5686 1.084 0.71 965.1
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 2.2 20.48 1.33 45044 2308 99.86 0.1929 0.1907 0.1913 0.2314 0.2315 56.27
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 16.1654 f_angle_d 1.3317 f_chiral_restr 0.0704 f_plane_restr 0.0131 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4803 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing