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Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.056 α = 90 b = 49.238 β = 90 c = 83.035 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 2013-11-05 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) Rrim I (All) 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 1.4 42.4 91.9 0.054 0.072 10.86 2.18 206127 -3 19.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.49 91.4 0.54 0.73 1.66
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 4PMX 1.401 42.35 112589 5631 98.26 0.1761 0.1745 0.1743 0.2054 0.2052 RANDOM 14.922
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] 0.09 -0.01 0.1 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.55 r_sphericity_free 22.571 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_3_deg 11.602 r_sphericity_bonded 9.831 r_dihedral_angle_1_deg 5.103 r_mcangle_it 1.222 r_scbond_it 1.117 r_angle_refined_deg 0.999 r_mcbond_it 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.55 r_sphericity_free 22.571 r_dihedral_angle_4_deg 15.68 r_dihedral_angle_3_deg 11.602 r_sphericity_bonded 9.831 r_dihedral_angle_1_deg 5.103 r_mcangle_it 1.222 r_scbond_it 1.117 r_angle_refined_deg 0.999 r_mcbond_it 0.896 r_rigid_bond_restr 0.613 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4840 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 38
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction