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Structure of mosquitocidal Cyt1Aa protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 10
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 10.3 300 In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid.
Crystal Properties Matthews coefficient Solvent content 1.91 35.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.446 α = 90 b = 65.446 β = 90 c = 165.451 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 PIXEL CS-PAD CXI-2 2018-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.28 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 120 1.7 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 19924 19924
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 MESH 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 1.85 50 99.9 0.998 0.07 34.6 165.4 18439
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 1.85 1.88 100 0.073 0.495 33.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6t14 1.85 26.824 18437 924 98.404 0.245 0.2426 0.2426 0.2937 0.294 34.123
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] -0.001 -0.001 -0.001 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.236 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_4_deg 7.819 r_dihedral_angle_1_deg 5.375 r_lrange_it 4.24 r_mcangle_it 0.892 r_angle_refined_deg 0.787 r_scangle_it 0.547 r_mcbond_it 0.48 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.236 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_4_deg 7.819 r_dihedral_angle_1_deg 5.375 r_lrange_it 4.24 r_mcangle_it 0.892 r_angle_refined_deg 0.787 r_scangle_it 0.547 r_mcbond_it 0.48 r_nbtor_refined 0.297 r_scbond_it 0.289 r_nbd_refined 0.197 r_symmetry_metal_ion_refined 0.187 r_metal_ion_refined 0.171 r_symmetry_nbd_refined 0.151 r_xyhbond_nbd_refined 0.089 r_symmetry_xyhbond_nbd_refined 0.077 r_chiral_restr 0.056 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1872 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing