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Crystal Structure of the B subunit of heat labile enterotoxin LT-IIc from Escherichia coli in complex with Sialyl-lacto-N-neotetraose d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 1.5 M LiSO4 100 mM Mes pH 6.5 and soaked in 2.5 M LiSO4 for cryoprotection prior mounting in cryoloop
Crystal Properties Matthews coefficient Solvent content 2.45 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.09 α = 90 b = 121.269 β = 90 c = 126.732 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2021-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 39.9 100 0.061 0.068 0.03 0.999 19 9.8 76810 30.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 99.9 0.645 0.718 0.314 0.934 3.3 10
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7PRP 2 38.541 76730 4010 99.939 0.19 0.1875 0.196 0.2297 0.2355 35.705
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] -1.995 1.588 0.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.645 r_dihedral_angle_4_deg 15.61 r_dihedral_angle_3_deg 11.994 r_lrange_it 6.612 r_lrange_other 6.568 r_dihedral_angle_1_deg 6.433 r_scangle_it 4.7 r_scangle_other 4.639 r_mcangle_other 3.25 r_mcangle_it 3.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.645 r_dihedral_angle_4_deg 15.61 r_dihedral_angle_3_deg 11.994 r_lrange_it 6.612 r_lrange_other 6.568 r_dihedral_angle_1_deg 6.433 r_scangle_it 4.7 r_scangle_other 4.639 r_mcangle_other 3.25 r_mcangle_it 3.248 r_scbond_it 3.173 r_scbond_other 3.128 r_mcbond_it 2.385 r_mcbond_other 2.376 r_angle_refined_deg 1.772 r_angle_other_deg 1.484 r_nbd_other 0.263 r_symmetry_xyhbond_nbd_refined 0.189 r_nbd_refined 0.187 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.167 r_xyhbond_nbd_other 0.152 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.135 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_ncsr_local_group_36 0.074 r_ncsr_local_group_26 0.066 r_ncsr_local_group_5 0.064 r_ncsr_local_group_20 0.064 r_ncsr_local_group_14 0.063 r_ncsr_local_group_42 0.063 r_ncsr_local_group_13 0.061 r_ncsr_local_group_23 0.061 r_ncsr_local_group_29 0.061 r_ncsr_local_group_34 0.061 r_ncsr_local_group_8 0.06 r_ncsr_local_group_39 0.06 r_ncsr_local_group_40 0.06 r_ncsr_local_group_30 0.059 r_ncsr_local_group_32 0.059 r_ncsr_local_group_37 0.059 r_ncsr_local_group_6 0.058 r_ncsr_local_group_31 0.058 r_ncsr_local_group_43 0.058 r_ncsr_local_group_41 0.056 r_ncsr_local_group_9 0.054 r_ncsr_local_group_16 0.053 r_ncsr_local_group_44 0.053 r_ncsr_local_group_10 0.052 r_ncsr_local_group_11 0.052 r_ncsr_local_group_21 0.051 r_ncsr_local_group_35 0.051 r_ncsr_local_group_24 0.05 r_ncsr_local_group_38 0.05 r_ncsr_local_group_3 0.049 r_ncsr_local_group_17 0.049 r_ncsr_local_group_25 0.048 r_ncsr_local_group_28 0.048 r_ncsr_local_group_45 0.046 r_ncsr_local_group_2 0.045 r_ncsr_local_group_19 0.045 r_ncsr_local_group_22 0.045 r_ncsr_local_group_27 0.045 r_ncsr_local_group_1 0.04 r_ncsr_local_group_15 0.038 r_ncsr_local_group_4 0.037 r_ncsr_local_group_7 0.037 r_ncsr_local_group_12 0.037 r_ncsr_local_group_18 0.036 r_ncsr_local_group_33 0.023 r_bond_refined_d 0.016 r_symmetry_xyhbond_nbd_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7477 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 330
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing