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Crystal structure of family 10 xylanase from Bacillus halodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.2M Magnesium chloride, 0.1M Hepes pH 7, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.45 α = 90 b = 42.353 β = 98.592 c = 58.769 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 100 IMAGE PLATE RIGAKU RAXIS IV++ 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU R-AXIS 1.54
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 2.21 50 98.3 0.073 0.073 19.89 6.4 19247 -3 27.6527547759
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 2.21 2.25 93.6 0.219 0.219 8.02 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2UWF 2.21357153532 39.1679388347 1.34754042894 19247 936 98.3947650938 0.167369570685 0.165149631138 0.1678 0.209115400246 0.2121 29.3013295677
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.0497481105 f_angle_d 0.818837922449 f_chiral_restr 0.0504603043386 f_bond_d 0.0069528564461 f_plane_restr 0.0050409211211
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2896 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing