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Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 303 Cry1Aa was expressed in the Bt cells by inoculating 250 mL of NYS medium and cultured at 303K for 3 days
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.7 α = 90 b = 88.7 β = 90 c = 270.19 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 100 PIXEL DECTRIS PILATUS3 6M 2020-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
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 3.6 50 100 0.689 0.4754 2.5 55.9 13301
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 3.6 3.63 100 0.657 0.7328 1.55 39.9
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 3.6 39.82 12547 668 99.75 0.22246 0.21733 0.2242 0.31764 0.3211 RANDOM 5.22
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] -0.9 -0.9 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.45 r_dihedral_angle_1_deg 7.897 r_dihedral_angle_2_deg 4.817 r_angle_refined_deg 1.003 r_long_range_B_refined 0.965 r_long_range_B_other 0.965 r_mcangle_it 0.359 r_mcangle_other 0.359 r_angle_other_deg 0.352 r_scangle_other 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.45 r_dihedral_angle_1_deg 7.897 r_dihedral_angle_2_deg 4.817 r_angle_refined_deg 1.003 r_long_range_B_refined 0.965 r_long_range_B_other 0.965 r_mcangle_it 0.359 r_mcangle_other 0.359 r_angle_other_deg 0.352 r_scangle_other 0.198 r_mcbond_it 0.191 r_mcbond_other 0.191 r_scbond_it 0.092 r_scbond_other 0.092 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 8075 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data scaling Coot model building XDS data reduction PHASER phasing