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Porcine E.coli heat-labile enterotoxin B-pentamer in complex with Lacto-N-neohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M sodium acetate, 20 % w/v PEG 6000, 0.2 M lithium chloride
Crystal Properties Matthews coefficient Solvent content 1.95 37.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.079 α = 90 b = 65.587 β = 108.64 c = 96.266 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 PIXEL DECTRIS PILATUS3 X 2M 2015-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 1.45 68.73 99.8 0.125 6.4 4.4 160263
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 1.45 1.47 1.151
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 1DJR 1.45 68.73 152246 7973 99.45 0.17653 0.17524 0.184 0.20087 0.2071 RANDOM 18.482
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] 0.14 -0.04 -0.14 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.517 r_dihedral_angle_4_deg 25.905 r_dihedral_angle_1_deg 15.187 r_dihedral_angle_3_deg 14.407 r_long_range_B_other 10.599 r_long_range_B_refined 10.594 r_scangle_other 10.423 r_scbond_it 9.34 r_scbond_other 9.339 r_mcangle_it 5.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.517 r_dihedral_angle_4_deg 25.905 r_dihedral_angle_1_deg 15.187 r_dihedral_angle_3_deg 14.407 r_long_range_B_other 10.599 r_long_range_B_refined 10.594 r_scangle_other 10.423 r_scbond_it 9.34 r_scbond_other 9.339 r_mcangle_it 5.262 r_mcangle_other 5.262 r_mcbond_it 4.543 r_mcbond_other 4.543 r_angle_refined_deg 1.682 r_angle_other_deg 1.393 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 8130 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data reduction Aimless data scaling PHASER phasing Coot model building