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Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4
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 16% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.2 44.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.235 α = 90 b = 66.028 β = 105.8 c = 78.642 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 2003-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9626 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 94.2 0.081 13.5 3.5 111363 104314 -3 13.4
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 69.3 0.591 1.8 2.7 7606
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 49.39 104314 104314 5219 93.89 0.13439 0.13439 0.13232 0.157 0.17389 0.1897 RANDOM 10.455
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] 0.04 0.03 -0.06 0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 21.151 r_scangle_it 7.194 r_dihedral_angle_1_deg 6.954 r_sphericity_bonded 6.669 r_scbond_it 5.237 r_mcangle_it 3.398 r_mcbond_it 2.485 r_rigid_bond_restr 2.121 r_angle_refined_deg 1.417 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 21.151 r_scangle_it 7.194 r_dihedral_angle_1_deg 6.954 r_sphericity_bonded 6.669 r_scbond_it 5.237 r_mcangle_it 3.398 r_mcbond_it 2.485 r_rigid_bond_restr 2.121 r_angle_refined_deg 1.417 r_angle_other_deg 0.862 r_symmetry_vdw_other 0.348 r_nbd_other 0.298 r_symmetry_hbond_refined 0.265 r_symmetry_vdw_refined 0.23 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.086 r_nbtor_other 0.086 r_bond_refined_d 0.012 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 4074 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling XTALVIEW refinement