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Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M MES pH 6, 30% PEG 400, 3% PGA-LM
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.245 α = 90 b = 66.476 β = 116.96 c = 82.401 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 PIXEL DECTRIS PILATUS3 6M 2015-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97239 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.2 45.6 93.8 0.096 0.994 5.55 2.9 144269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 72.4 0.337 2.3
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 3CHB 1.2 73.45 136978 7295 93.95 0.19671 0.19506 0.1993 0.22817 0.2333 RANDOM 17.371
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] -0.84 0.02 -0.64 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_4_deg 26.349 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_1_deg 7.094 r_long_range_B_refined 5.342 r_long_range_B_other 5.341 r_scangle_other 3.666 r_mcangle_it 2.681 r_mcangle_other 2.681 r_scbond_it 2.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.169 r_dihedral_angle_4_deg 26.349 r_dihedral_angle_3_deg 14.41 r_dihedral_angle_1_deg 7.094 r_long_range_B_refined 5.342 r_long_range_B_other 5.341 r_scangle_other 3.666 r_mcangle_it 2.681 r_mcangle_other 2.681 r_scbond_it 2.395 r_scbond_other 2.392 r_angle_refined_deg 2.154 r_mcbond_it 1.764 r_mcbond_other 1.753 r_angle_other_deg 1.144 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4085 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing