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Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263N mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WU4 PDB ENTRY 1WU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG4000, SODIUM ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.182 α = 90 b = 86.235 β = 90 c = 87.585 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 ADSC QUANTUM 210 2005-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.6 61.43 99.4 0.061 27.9 5 53903 53617 15.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 98.8 0.236 3.1 4.4 5260
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1WU4 1.6 40.23 50897 50897 2719 99.48 0.1627 0.1627 0.16173 0.1584 0.18164 0.1782 RANDOM 16.718
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] 0.06 -0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_3_deg 11.992 r_dihedral_angle_4_deg 9.464 r_dihedral_angle_1_deg 5.566 r_scangle_it 3.079 r_scbond_it 1.904 r_mcangle_it 1.201 r_angle_refined_deg 1.157 r_mcbond_it 0.704 r_symmetry_hbond_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_3_deg 11.992 r_dihedral_angle_4_deg 9.464 r_dihedral_angle_1_deg 5.566 r_scangle_it 3.079 r_scbond_it 1.904 r_mcangle_it 1.201 r_angle_refined_deg 1.157 r_mcbond_it 0.704 r_symmetry_hbond_refined 0.33 r_nbtor_refined 0.314 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3085 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling