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Cry3A Toxin structure obtained by injecting Bacillus thuringiensis cells in an XFEL beam, collecting data by serial femtosecond crystallographic methods and processing data with the cctbx.xfel software suite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLC PDB ENTRY 1DLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN VIVO CRYSTALLIZATION 303 Cry3A crystallized within the bacterial cell, IN VIVO CRYSTALLIZATION, temperature 303K
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.05 α = 90 b = 134.76 β = 90 c = 104.85 γ = 90
Symmetry Space Group C 2 2 21
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 Cornell-SLAC Pixel Array Detector (CSPAD) 2013-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.457 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 52.42 92.3 0.216 59.2 252.5 18583 18583 30.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.99 39.2 0.906 2.3 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1DLC 2.9 52.42 18583 18583 931 99.14 0.1699 0.1683 0.1887 0.2013 0.2257 RANDOM 38.39
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] 0.6597 1.3849 -2.0446
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.95 t_omega_torsion 2.52 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.95 t_omega_torsion 2.52 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4659 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction cctbx.xfel data reduction BUSTER refinement