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Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CHB PDB ENTRY 3CHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 12% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.2 44.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.09 α = 90 b = 66.079 β = 105.83 c = 78.715 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2003-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9791 ALS 8.2.2
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 1.35 50 91.3 0.059 19.5 3.66 105335 100384 -3 12.9
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) 1.35 1.4 63.8 0.451 2.4 3.22 6952
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 (All) 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 PDB ENTRY 3CHB 1.35 48.22 100384 100384 5029 91.22 0.13194 0.13194 0.12986 0.1499 0.17052 0.1861 RANDOM 10.928
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] -0.06 -0.03 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 21.699 r_dihedral_angle_1_deg 6.952 r_scangle_it 6.083 r_sphericity_bonded 6.002 r_scbond_it 4.376 r_mcangle_it 3.476 r_mcbond_it 2.658 r_rigid_bond_restr 2.112 r_angle_refined_deg 1.501 r_angle_other_deg 0.867
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 21.699 r_dihedral_angle_1_deg 6.952 r_scangle_it 6.083 r_sphericity_bonded 6.002 r_scbond_it 4.376 r_mcangle_it 3.476 r_mcbond_it 2.658 r_rigid_bond_restr 2.112 r_angle_refined_deg 1.501 r_angle_other_deg 0.867 r_symmetry_vdw_other 0.355 r_nbd_other 0.297 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.176 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.088 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4093 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling XTALVIEW refinement