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Structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals soaked with DTT at pH 7
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 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 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.562 α = 90 b = 65.562 β = 90 c = 164.305 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 18766 18766
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 1.83 50 99.9 0.998 0.074 32.8 160.5 18261
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 1.83 1.85 100 0.164 0.517 3 30.8
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 14.838 18260 921 97.767 0.227 0.2241 0.2265 0.2901 0.2932 32.369
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] 0.008 0.004 0.008 -0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.027 r_dihedral_angle_3_deg 14.734 r_lrange_it 6.038 r_lrange_other 5.458 r_dihedral_angle_1_deg 5.42 r_dihedral_angle_4_deg 2.753 r_mcangle_it 1.836 r_mcangle_other 1.835 r_scangle_it 1.77 r_scangle_other 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.027 r_dihedral_angle_3_deg 14.734 r_lrange_it 6.038 r_lrange_other 5.458 r_dihedral_angle_1_deg 5.42 r_dihedral_angle_4_deg 2.753 r_mcangle_it 1.836 r_mcangle_other 1.835 r_scangle_it 1.77 r_scangle_other 1.77 r_angle_other_deg 1.382 r_scbond_it 1.103 r_scbond_other 1.102 r_mcbond_it 1.078 r_mcbond_other 1.078 r_angle_refined_deg 0.799 r_symmetry_nbd_other 0.216 r_nbd_other 0.19 r_nbd_refined 0.186 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.108 r_symmetry_xyhbond_nbd_refined 0.098 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.003 r_gen_planes_other 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing