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Crystal structure of acetyl xylan esterase from Bacillus pumilus obtained in presence of D-xylose and sodium acetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVT PDB entry 3FVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 293 0.3M lithium chloride, 0.2M sodium acetate, 0.2M D-xylose, 5% PEG 6000, 0.05M MES, pH 6.0, microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.225 α = 90 b = 86.622 β = 112.78 c = 183.973 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 CCD MAR CCD 165 mm 2004-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.200 ELETTRA 5.2R
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 2.62 30 86.9 0.097 2.9 106905 106905 -3 36.49
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) 2.62 2.72 80.6 0.362 3.3 2.7 8208
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3FVT 2.62 26.88 106893 106893 10592 86 0.196 0.196 0.196 0.1855 0.23 0.2183 RANDOM 19.338
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] 6.644 -4.255 -0.171 -6.474
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.594 c_scbond_it 1.716 c_mcangle_it 1.599 c_angle_deg 1.234 c_mcbond_it 1.003 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30418 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 160
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction MAR345 data collection CNS phasing