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Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263C 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 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.242 α = 90 b = 86.369 β = 90 c = 87.653 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 1.7 61.546 98.5 0.064 27.45 5 45145 44431 18.2
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 1.7 1.76 99.6 0.358 4.1 4.8 4438
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 1.7 39.07 42177 42177 2252 98.53 0.1623 0.1623 0.16103 0.1585 0.18731 0.1865 RANDOM 18.68
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] 0.07 -0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.96 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_4_deg 10.984 r_dihedral_angle_1_deg 5.509 r_scangle_it 3.303 r_scbond_it 2.063 r_mcangle_it 1.24 r_angle_refined_deg 1.195 r_mcbond_it 0.758 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.96 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_4_deg 10.984 r_dihedral_angle_1_deg 5.509 r_scangle_it 3.303 r_scbond_it 2.063 r_mcangle_it 1.24 r_angle_refined_deg 1.195 r_mcbond_it 0.758 r_nbtor_refined 0.313 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.184 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.088 r_bond_refined_d 0.011 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 3083 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling