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Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri in the native form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.463 α = 90 b = 71.834 β = 90 c = 83.839 γ = 90
Symmetry Space Group P 21 21 21
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 1.03 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 1.3 50 94.4 0.04 13.5 2.9 69082
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 1.3 1.32 95.5 0.561 3 3442
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.304 41.95 68887 1873 93.68 0.1333 0.1322 0.1327 0.1743 0.1742 RANDOM 14.16
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] -0.08 0.06 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.407 r_dihedral_angle_2_deg 33.682 r_dihedral_angle_4_deg 19.021 r_dihedral_angle_3_deg 11.724 r_sphericity_bonded 10.625 r_dihedral_angle_1_deg 5.948 r_rigid_bond_restr 5.935 r_mcangle_it 2.688 r_mcbond_it 2.357 r_mcbond_other 2.243
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.407 r_dihedral_angle_2_deg 33.682 r_dihedral_angle_4_deg 19.021 r_dihedral_angle_3_deg 11.724 r_sphericity_bonded 10.625 r_dihedral_angle_1_deg 5.948 r_rigid_bond_restr 5.935 r_mcangle_it 2.688 r_mcbond_it 2.357 r_mcbond_other 2.243 r_angle_refined_deg 2.02 r_angle_other_deg 0.991 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2436 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PDB_EXTRACT data extraction