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Crystal structure of a putative polysaccharide deacetylase involved in o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 20.0000% MPD, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.3 62.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.724 α = 90 b = 74.724 β = 90 c = 142.692 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-12-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97985,0.97968 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 1.9 29.566 100 0.085 0.085 0.091 15.5 7.2 32707 29.568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.902 0.902 0.971 2.1 7.3 2365
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.9 29.566 32639 1654 99.98 0.163 0.162 0.1683 0.184 0.1913 RANDOM 38.386
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] 0.6 0.6 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.329 r_dihedral_angle_4_deg 14.965 r_dihedral_angle_3_deg 12.131 r_scangle_it 5.929 r_dihedral_angle_1_deg 4.564 r_scbond_it 4.458 r_mcangle_it 2.584 r_mcbond_it 1.791 r_angle_refined_deg 1.437 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.329 r_dihedral_angle_4_deg 14.965 r_dihedral_angle_3_deg 12.131 r_scangle_it 5.929 r_dihedral_angle_1_deg 4.564 r_scbond_it 4.458 r_mcangle_it 2.584 r_mcbond_it 1.791 r_angle_refined_deg 1.437 r_angle_other_deg 0.918 r_mcbond_other 0.455 r_symmetry_vdw_other 0.296 r_symmetry_vdw_refined 0.266 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.215 r_nbd_other 0.213 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.092 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1971 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing