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Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Galactoside 2a
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 7.8 298 32% PEG 5000, 100 mM Tris-HCl pH 7.8, 50 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.96 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.817 α = 90 b = 78.683 β = 116.2 c = 62.3 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 CCD SBC-2 2002-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.99 50 95.3 0.061 19.28 3.45 34499 34499 20.322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.99 2.07 84.1 0.145 7.07 2.27 3005
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1DJR 1.99 27.95 34499 32749 1731 95.21 0.15778 0.15778 0.15449 0.2207 0.2446 RANDOM 15.815
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] 0.01 0.03 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.338 r_scangle_it 4.461 r_scbond_it 3.017 r_mcangle_it 2.433 r_mcbond_it 1.656 r_angle_refined_deg 1.158 r_angle_other_deg 0.651 r_symmetry_vdw_other 0.304 r_symmetry_vdw_refined 0.297 r_nbd_other 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.338 r_scangle_it 4.461 r_scbond_it 3.017 r_mcangle_it 2.433 r_mcbond_it 1.656 r_angle_refined_deg 1.158 r_angle_other_deg 0.651 r_symmetry_vdw_other 0.304 r_symmetry_vdw_refined 0.297 r_nbd_other 0.29 r_symmetry_hbond_refined 0.244 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.21 r_nbtor_other 0.088 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement TRUNCATE data reduction XTALVIEW refinement HKL-2000 data collection HKL-2000 data reduction CCP4 data scaling