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Full-length Cholix toxin from Vibrio Cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKQ Domain I and II of Pseudomonas exotoxin A - PDB entry 1IKQ. Domain III (the catalytic fragment of Cholix - PDB ENTRY ?)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 23% PEG 10.000, 7.5% Ethylene Glycol, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.936 α = 90 b = 88.338 β = 95.32 c = 79.934 γ = 90
Symmetry Space Group P 1 21 1
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 Bruker Platinum 135 2007-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 50 98.1 0.0944 8.62 3.9 44284 43440
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.15 88.8 0.5151 1.31 1.97
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Domain I and II of Pseudomonas exotoxin A - PDB entry 1IKQ.
Domain III (the catalytic fragment of Cholix - PDB ENTRY ?) 2.1 33.31 38766 2059 99.09 0.19371 0.19128 0.1922 0.23925 0.2401 RANDOM 16.914
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] 0.1 -0.04 -0.14 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.883 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 16.544 r_dihedral_angle_1_deg 6.18 r_scangle_it 2.01 r_scbond_it 1.292 r_angle_refined_deg 1.031 r_mcangle_it 0.81 r_mcbond_it 0.474 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.883 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 16.544 r_dihedral_angle_1_deg 6.18 r_scangle_it 2.01 r_scbond_it 1.292 r_angle_refined_deg 1.031 r_mcangle_it 0.81 r_mcbond_it 0.474 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.076 r_bond_refined_d 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4745 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 38
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM2 data collection PROTEUM2 data reduction