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Crystal structure of human heat-labile enterotoxin in complex with a blood group A antigen analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DJR
Crystallization Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.799 α = 90 b = 166.965 β = 90 c = 57.478 γ = 90
Symmetry Space Group P 21 21 2
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 MAR CCD 165 mm mirrors 2005-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 0.907 MAX II I911-5
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 2.5 96.2 99 0.033 24.9 6.1 38366
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 2.53 2.6 94.2 0.08 12.4 3.7
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 2.53 20 36444 1922 99.05 0.18351 0.1807 0.1942 0.23703 0.2438 RANDOM 13.367
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] 0.76 -0.36 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 19.501 r_dihedral_angle_3_deg 14.983 r_dihedral_angle_1_deg 6.456 r_scangle_it 1.835 r_angle_other_deg 1.561 r_angle_refined_deg 1.45 r_scbond_it 1.327 r_mcangle_it 0.847 r_mcbond_it 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 19.501 r_dihedral_angle_3_deg 14.983 r_dihedral_angle_1_deg 6.456 r_scangle_it 1.835 r_angle_other_deg 1.561 r_angle_refined_deg 1.45 r_scbond_it 1.327 r_mcangle_it 0.847 r_mcbond_it 0.754 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.232 r_symmetry_vdw_other 0.211 r_nbd_other 0.204 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.097 r_nbtor_other 0.097 r_mcbond_other 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8045 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 570
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing