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native structure of full-length pesticidal protein Cry1Ca18 at pH9, from crystals formed in vivo
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 1.96 37.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.8 α = 90 b = 88.8 β = 90 c = 267.82 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
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 1.65 26.91 100 0.9986875 23.214064 1379 122789 17.8
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 1.65 1.69 100 0.18 0.44
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 1.65 26.91 122231 6387 99.42 0.17906 0.17762 0.1859 0.2064 0.2131 RANDOM 25.476
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] -0.58 -0.58 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.968 r_dihedral_angle_2_deg 7.933 r_dihedral_angle_1_deg 6.897 r_long_range_B_refined 6.565 r_long_range_B_other 6.462 r_scangle_other 2.306 r_angle_refined_deg 1.745 r_mcangle_it 1.52 r_mcangle_other 1.52 r_scbond_it 1.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.968 r_dihedral_angle_2_deg 7.933 r_dihedral_angle_1_deg 6.897 r_long_range_B_refined 6.565 r_long_range_B_other 6.462 r_scangle_other 2.306 r_angle_refined_deg 1.745 r_mcangle_it 1.52 r_mcangle_other 1.52 r_scbond_it 1.393 r_scbond_other 1.392 r_mcbond_it 0.867 r_mcbond_other 0.867 r_angle_other_deg 0.631 r_chiral_restr 0.095 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 8519 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CrystFEL data scaling PHASER phasing PDB_EXTRACT data extraction CrystFEL data reduction