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native structure of the full-length pesticidal protein Cry8Ba2, from crystals formed in vivo (form 2)
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EB7 DI - DIII used experimental model PDB 4W8J DIV - DVII used
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 7 298 Natural conditions
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.32 α = 90 b = 93.32 β = 90 c = 275.51 γ = 90
Symmetry Space Group P 41 21 2
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 2022-05-09 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
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 DFFN 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 2.2 28.17 98.031 0.987 0.145 6 226.21 61661
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 2.23 0.088 3.02 0.74
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.27 28.11 54383 2896 99.91 0.18244 0.18014 0.1852 0.22585 0.2269 RANDOM 55.054
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.401 r_dihedral_angle_2_deg 7.442 r_dihedral_angle_1_deg 7.276 r_long_range_B_other 6.363 r_long_range_B_refined 6.362 r_scangle_other 3.994 r_mcangle_it 3.38 r_mcangle_other 3.38 r_scbond_it 2.388 r_scbond_other 2.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.401 r_dihedral_angle_2_deg 7.442 r_dihedral_angle_1_deg 7.276 r_long_range_B_other 6.363 r_long_range_B_refined 6.362 r_scangle_other 3.994 r_mcangle_it 3.38 r_mcangle_other 3.38 r_scbond_it 2.388 r_scbond_other 2.388 r_mcbond_it 2.016 r_mcbond_other 2.015 r_angle_refined_deg 1.577 r_angle_other_deg 0.56 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9176 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing CrystFEL data reduction CrystFEL data scaling