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Crystal structure of mutant (D248N) Salmonella typhimurium family 3 glycoside hydrolase (NagZ) in complex with GlcNAc-1,6-anhMurNAc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 296 0.1 M MES, 25% PEG 1000 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.67 α = 90 b = 65.64 β = 99.24 c = 94.91 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 IMAGE PLATE RIGAKU RAXIS IV 2010-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 28.49 97.1 0.034 0.04 19.1 3.5 84880 3 17.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 81.1 0.149 0.192 4.6 2.5
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.55 28.36 1.36 84880 84812 2553 97 0.172 0.171 0.1652 0.202 0.1941
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] -4.5693 0.9479 7.1338 -2.5645
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.581 f_angle_d 1.182 f_chiral_restr 0.07 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5077 Nucleic Acid Atoms Solvent Atoms 783 Heterogen Atoms 78
Software Software Software Name Purpose CrystalClear data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing