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The mechanism by which arabinoxylanases can recognise highly decorated xylans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 100 mM Tris-Bicine buffer pH 8.5, 12.5% (w/v) polyethylene glycol average Mw 1,000 Da, 12.5% (w/v) polyethylene glycol average Mw 3,350 Da and 12.5% (RS)-2-methyl-2,4-pentanediol (racemic).
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.273 α = 90 b = 123.176 β = 90 c = 125.38 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 PIXEL DECTRIS PILATUS3 6M 2015-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9791 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.65 48.43 99.8 0.057 0.988 11.2 3.3 140288 1.5
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 1.65 1.68 99.4 0.749 1.6 3.4
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 (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 5AK1 1.65 48.43 133265 6940 98.6 0.14901 0.14637 0.1594 0.19855 0.2068 RANDOM 21.695
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] -0.59 0.7 -0.12
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.455 r_dihedral_angle_2_deg 33.549 r_dihedral_angle_4_deg 16.097 r_dihedral_angle_3_deg 11.761 r_sphericity_bonded 9.352 r_dihedral_angle_1_deg 6.39 r_long_range_B_refined 4.771 r_long_range_B_other 3.891 r_scangle_other 2.94 r_mcangle_other 2.596
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.455 r_dihedral_angle_2_deg 33.549 r_dihedral_angle_4_deg 16.097 r_dihedral_angle_3_deg 11.761 r_sphericity_bonded 9.352 r_dihedral_angle_1_deg 6.39 r_long_range_B_refined 4.771 r_long_range_B_other 3.891 r_scangle_other 2.94 r_mcangle_other 2.596 r_mcangle_it 2.594 r_scbond_it 2.583 r_scbond_other 2.579 r_mcbond_it 2.178 r_mcbond_other 2.175 r_rigid_bond_restr 2.081 r_angle_refined_deg 1.533 r_angle_other_deg 0.972 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7241 Nucleic Acid Atoms Solvent Atoms 923 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction XDS data scaling