Navigation Tabs The structure of natural crystals of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated using serial femtosecond crystallography at an X-ray free electron laser
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WA1 3WA1, 5FOY, 5G37 experimental model PDB 5FOY 3WA1, 5FOY, 5G37 experimental model PDB 5G37 3WA1, 5FOY, 5G37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 298 Natural crystallisation
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.76 α = 90 b = 83.15 β = 90 c = 157.33 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 293 PIXEL AGIPD 2021-10-18 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 Double flow focusing nozzle (DFFN) injection
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 3D printed DFFN (CFEL) undefined (µl/min) undefined (µm) DFFN
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 28.57 100 0.99 0.12 8.91 485 53943
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 2.22 100 0.48 0.918 1.25 28.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3WA1, 5FOY, 5G37 2.2 28.57 52112 1755 99.93 0.1611 0.1599 0.17 0.1967 0.2 RANDOM 31.759
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] -0.07 0.58 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 14.739 r_dihedral_angle_1_deg 7.533 r_angle_refined_deg 1.848 r_angle_other_deg 1.321 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_4_deg 18.811 r_dihedral_angle_3_deg 14.739 r_dihedral_angle_1_deg 7.533 r_angle_refined_deg 1.848 r_angle_other_deg 1.321 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6748 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling PHASER phasing PHENIX refinement PHENIX model building
