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Crystal structure of a glycoside hydrolase family 11 xylanase from Aspergillus niger in complex with xylopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 1.6M ammonium sulphate, 0.1M HEPES pH 7.5, 0.1 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.326 α = 90 b = 67.326 β = 90 c = 165.401 γ = 120
Symmetry Space Group P 65 2 2
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 MAR CCD 165 mm 2006-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9918 EMBL/DESY, HAMBURG BW7A
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 2.8 30 98.2 0.094 13.7 6010 5843 2 1.4
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) 2.8 2.85 98.2 0.302 5.3 271
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UKR 2.8 19.48 5220 5219 542 97.31 0.22632 0.2212 0.2207 0.27678 0.2738 RANDOM 23.812
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] 0.04 0.71 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 31.141 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.212 r_angle_refined_deg 1.005 r_sphericity_free 0.931 r_scangle_it 0.595 r_mcangle_it 0.564 r_scbond_it 0.356 r_rigid_bond_restr 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.048 r_dihedral_angle_4_deg 31.141 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 6.212 r_angle_refined_deg 1.005 r_sphericity_free 0.931 r_scangle_it 0.595 r_mcangle_it 0.564 r_scbond_it 0.356 r_rigid_bond_restr 0.333 r_mcbond_it 0.312 r_nbtor_refined 0.31 r_sphericity_bonded 0.267 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.064 r_metal_ion_refined 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1402 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling PHASER phasing