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Structure and mode of action of a mosquitocidal holotoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CB4 PDB ENTRY 2CB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.3 0.1 M TRIS, PH 8.3 3% (W/V) PEG-6000 250 MM KCL 4% MPD
Crystal Properties Matthews coefficient Solvent content 3.4 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.963 α = 90 b = 130.963 β = 90 c = 396.061 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 100 CCD MARREASEARCH 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 75 99.9 0.09 0.084 18.6 7.1 87586 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.58 99.8 0.38 0.48 3.3 5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CB4 2.5 74.54 83206 4379 100 0.194 0.192 0.234 0.2757 RANDOM 49.23
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] 1.46 0.73 1.46 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.53 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 6.63 r_scangle_it 1.646 r_angle_refined_deg 1.201 r_scbond_it 1.072 r_mcangle_it 0.556 r_nbtor_refined 0.309 r_mcbond_it 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.53 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.837 r_dihedral_angle_1_deg 6.63 r_scangle_it 1.646 r_angle_refined_deg 1.201 r_scbond_it 1.072 r_mcangle_it 0.556 r_nbtor_refined 0.309 r_mcbond_it 0.302 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13480 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing