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Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M sodium cacodylate pH=6.5, 1.9M soduim acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.51 64.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.265 α = 90 b = 80.993 β = 91.95 c = 79.277 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2001-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.100 NSLS X26C
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 1.58 39.48 98.2 0.081 10.9 4.88 146371 143748 10.9 22.7
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 1.58 1.61 84.4 0.375 19.83 2.5 6107
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION using IXT6 native phases since only one mutation was done, the same space group and unit cell were obtained. Doing rigid and annealing. THROUGHOUT 2Q8X 1.58 39.48 143748 138364 6992 0.197 0.2127 0.209 0.2249 RANDOM 25.3
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] -6.74 -0.93 8.12 -1.38
RMS Deviations Key Refinement Restraint Deviation DIHEDRAL ANGLES 21.8 BOND ANGLES 1.3 IMPROPER ANGLES 0.81 BOND LENGTHS 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5391 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction CNS refinement SCALEPACK data scaling CNS phasing