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Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein at pH 7
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 7 298 Natural
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.65 α = 90 b = 83.11 β = 90 c = 156.91 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 298 PIXEL AGIPD 2022-04-22 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 injection
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 1.62 24.98 100 0.997 10.61 1028.3 132750
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 1.62 1.64 0.133
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 THROUGHOUT 3WA1, 5FOY, 5G37 1.62 24.98 125990 6673 99.95 0.1771 0.1762 0.1855 0.1947 0.2011 RANDOM 31.465
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.824 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_3_deg 13.112 r_dihedral_angle_1_deg 7.371 r_angle_refined_deg 1.439 r_angle_other_deg 1.354 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.824 r_dihedral_angle_4_deg 18.028 r_dihedral_angle_3_deg 13.112 r_dihedral_angle_1_deg 7.371 r_angle_refined_deg 1.439 r_angle_other_deg 1.354 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6748 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction CrystFEL data reduction CrystFEL data scaling