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The crystal structure of Stx2 and a disaccharide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R4P pdb entry 1R4P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 297 3.8 M sodium formate, 50 mM Tris pH 7.0, 2% ethylene glycol, and 1 mM PPS (3-(1-pyridino)-1-propanesulfonate) , VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.25 α = 90 b = 146.25 β = 90 c = 60.31 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2012-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97949 CLSI 08B1-1
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 1.56 50 92.8 0.082 8.8 206175 104677 -3
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 1.56 1.65 89.9 0.978 1.4 2.9 29975
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 (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 pdb entry 1R4P 1.56 40 99853 99444 5229 99.59 0.1714 0.17031 0.1876 0.19193 0.2014 RANDOM 25.06
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] -0.17 -0.09 -0.17 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 5.336 r_scangle_it 1.512 r_angle_refined_deg 0.989 r_scbond_it 0.943 r_mcangle_it 0.619 r_mcbond_it 0.32 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 11.644 r_dihedral_angle_1_deg 5.336 r_scangle_it 1.512 r_angle_refined_deg 0.989 r_scbond_it 0.943 r_mcangle_it 0.619 r_mcbond_it 0.32 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4961 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 93
Software Software Software Name Purpose MxDC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling