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Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl xylotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.1 41.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.709 α = 90 b = 142.709 β = 90 c = 72.454 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2019-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2 100 99.3 0.165 17.9 8.7 110677
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 2.07 0.839 2.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7DFM 2 47.061 110646 5434 99.239 0.168 0.1651 0.2176 0.2204 30.941
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] 0.856 0.428 0.856 -2.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.067 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 8.316 r_lrange_it 5.281 r_lrange_other 5.28 r_scangle_it 4.161 r_scangle_other 4.161 r_mcangle_it 2.978 r_mcangle_other 2.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.067 r_dihedral_angle_3_deg 13.709 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_1_deg 8.316 r_lrange_it 5.281 r_lrange_other 5.28 r_scangle_it 4.161 r_scangle_other 4.161 r_mcangle_it 2.978 r_mcangle_other 2.978 r_scbond_it 2.845 r_scbond_other 2.844 r_mcbond_it 2.256 r_mcbond_other 2.256 r_angle_refined_deg 1.577 r_angle_other_deg 1.365 r_nbd_other 0.217 r_metal_ion_refined 0.206 r_nbd_refined 0.185 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.145 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_xyhbond_nbd_other 0.089 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.059 r_symmetry_metal_ion_refined 0.057 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13486 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 328
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data scaling MOLREP phasing