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Crystal structure of a novel reducing-end xylose-releasing exo-oligoxylanase (XynA) belonging to GH10 family (space group P1211)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Polyethylene glycol 6000
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.022 α = 90 b = 100.741 β = 95.15 c = 134.199 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 MARMOSAIC 225 mm CCD 2013-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45 LNLS W01B-MX2
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 2.857 50 97.7 0.15 5.8 2.9 52305
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) 1 2.857 2.92 95.9 0.61 2.6 2589
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2CNC 2.857 41.15 52253 2651 97.17 0.2133 0.2107 0.2089 0.261 0.2578 RANDOM 45.864
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] 0.43 -0.33 -0.75 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.515 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_3_deg 15.284 r_dihedral_angle_1_deg 5.045 r_mcangle_it 1.105 r_angle_refined_deg 0.944 r_mcbond_it 0.629 r_scbond_it 0.618 r_chiral_restr 0.066 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.515 r_dihedral_angle_4_deg 18.849 r_dihedral_angle_3_deg 15.284 r_dihedral_angle_1_deg 5.045 r_mcangle_it 1.105 r_angle_refined_deg 0.944 r_mcbond_it 0.629 r_scbond_it 0.618 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16837 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction REFMAC refinement PDB_EXTRACT data extraction