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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 Na/K phosphate, 100 mM MES pH 6.5 and 2M NaCl.
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.911 α = 90 b = 72.514 β = 90 c = 109.537 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 PILATUS 6M 2012-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9772 Diamond I24
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 1.9 45.16 98.6 0.028 0.999 26.6 3.6 42716 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 1.9 1.94 85 0.084 8 2.1
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 1.9 45.16 40566 2090 98.37 0.13097 0.12944 0.1433 0.16041 0.1734 RANDOM 17.065
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] 1.3 -0.55 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 11.452 r_dihedral_angle_1_deg 6.199 r_long_range_B_refined 5.722 r_long_range_B_other 5.722 r_scangle_other 2.587 r_mcangle_other 1.646 r_mcangle_it 1.643 r_scbond_it 1.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 11.452 r_dihedral_angle_1_deg 6.199 r_long_range_B_refined 5.722 r_long_range_B_other 5.722 r_scangle_other 2.587 r_mcangle_other 1.646 r_mcangle_it 1.643 r_scbond_it 1.639 r_scbond_other 1.639 r_angle_refined_deg 1.621 r_mcbond_it 1.087 r_mcbond_other 1.072 r_angle_other_deg 0.992 r_chiral_restr 0.222 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing XDS data reduction