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Native structure of the full-length pesticidal protein Cry1Ca18 at pH7, from crystals formed in vivo
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W8J Cry1Ac
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 9 298 Naturally grown
Crystal Properties Matthews coefficient Solvent content 2.01 38.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.16 α = 90 b = 88.16 β = 90 c = 266.43 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 2023-05-11 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 1.8 36.19 100 0.9965445 13.75 207.97 98288
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 1.8 1.82 100 0.79 2.77
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 1.8 36.19 93379 4841 99.98 0.18353 0.18157 0.1894 0.22169 0.2286 RANDOM 18.835
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] -0.56 -0.56 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 6.863 r_dihedral_angle_2_deg 6.482 r_long_range_B_refined 4.853 r_long_range_B_other 4.807 r_angle_refined_deg 1.743 r_scangle_other 1.351 r_scbond_it 0.824 r_scbond_other 0.822 r_mcangle_it 0.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.574 r_dihedral_angle_1_deg 6.863 r_dihedral_angle_2_deg 6.482 r_long_range_B_refined 4.853 r_long_range_B_other 4.807 r_angle_refined_deg 1.743 r_scangle_other 1.351 r_scbond_it 0.824 r_scbond_other 0.822 r_mcangle_it 0.807 r_mcangle_other 0.807 r_angle_other_deg 0.613 r_mcbond_it 0.458 r_mcbond_other 0.458 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 8493 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystFEL data scaling PHASER phasing CrystFEL data reduction