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Crystal structure of GTB + UDP-Glc + H-antigen acceptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Grown in 1% polyethylene glycol (PEG) 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM N-[-acetamido]-2-iminodiacetic acid (ADA), 30 mM sodium acetate, 5 mM manganese chloride. Grown 5-10 days.
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.64 α = 90 b = 149.67 β = 90 c = 79.46 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV++ 2007-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.55 74.83 98.5 0.046 15.6 4.2 45267
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 1.55 1.61 99.7 0.273 3.7 3.49 4512
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 1LZ0 1.55 74.83 42973 2285 98.43 0.1744 0.1732 0.1868 0.1979 0.209 RANDOM 20.834
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] -0.75 0.12 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 12.348 r_dihedral_angle_1_deg 7.368 r_mcangle_it 1.964 r_angle_refined_deg 1.612 r_mcbond_it 1.267 r_mcbond_other 1.264 r_angle_other_deg 1.025 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 12.348 r_dihedral_angle_1_deg 7.368 r_mcangle_it 1.964 r_angle_refined_deg 1.612 r_mcbond_it 1.267 r_mcbond_other 1.264 r_angle_other_deg 1.025 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2360 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 61
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building PHASER phasing CrystalClear data reduction