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Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S 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 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.249 α = 90 b = 85.026 β = 90 c = 86.822 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 QUAMTUM 4r 2004-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
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 2.1 60.746 97.3 0.099 15.2 4.5 23314 22673 12.8
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 2.1 2.18 99.2 0.243 5.9 4.5 2294
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 2.1 43.4 21506 21506 1163 97.3 0.1437 0.1437 0.14013 0.1417 0.21041 0.2132 RANDOM 10.255
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] -0.02 0.03 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.678 r_dihedral_angle_4_deg 15.409 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.391 r_scbond_it 2.252 r_angle_refined_deg 1.406 r_mcangle_it 1.367 r_mcbond_it 0.848 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.678 r_dihedral_angle_4_deg 15.409 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.391 r_scbond_it 2.252 r_angle_refined_deg 1.406 r_mcangle_it 1.367 r_mcbond_it 0.848 r_nbtor_refined 0.313 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.203 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3106 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling