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Crystal structure of a novel thermostable GH10 xylanase XynA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 29% PEG 600 (w/v), 0.1 M CaCl2, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.59 52.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.842 α = 90 b = 109.842 β = 90 c = 85.57 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD ADSC QUANTUM 315r 2019-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 15.33 99.35 0.158 0.159 0.031 0.99 30 25.3 22405 51.0611188386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.345 2.429 0.99
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 1V0L 2.34482019351 15.3263372188 1.37661057842 22403 1124 99.8440146181 0.216210592416 0.214473386139 0.2162 0.248285153375 0.25 55.7565312641
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 10.2014162748 f_angle_d 0.965207165333 f_chiral_restr 0.0589742614023 f_bond_d 0.00829585145842 f_plane_restr 0.00566542691731
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing