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Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 16% (v/v) ethylene glycol, 8% (w/v) PEG 3350, 1mM TCEP, 50mM HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.85 78.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.829 α = 90 b = 136.829 β = 90 c = 119.268 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2004-06-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.3403, 1.3408, 1.3460 Photon Factory BL-5A
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 2.38 29.75 99.9 0.067 26.2 11 50770 62.5
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 2.38 2.51 99.8 0.451 4.2 10.6 7356
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 MAD THROUGHOUT 2.38 29.74 45647 5121 0.19377 0.19064 0.1849 0.22212 0.2148 RANDOM 58.421
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] 0.46 0.23 0.46 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.129 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 6.436 r_scangle_it 2.605 r_scbond_it 1.643 r_angle_refined_deg 1.337 r_mcangle_it 1.076 r_mcbond_it 0.615 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.129 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 14.903 r_dihedral_angle_1_deg 6.436 r_scangle_it 2.605 r_scbond_it 1.643 r_angle_refined_deg 1.337 r_mcangle_it 1.076 r_mcbond_it 0.615 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3806 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing