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Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M TRIS (PH 7.8), 0.3 M POTASSIUM BROMIDE, 8 % PGA-LM
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.89 α = 90 b = 131.91 β = 90 c = 73.17 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M-F 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.28 73.17 99.8 0.13 11.4 6.5 39506 2
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 2.28 2.34 99.6 0.62 2.8 6.6
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 4LGN 2.28 73.17 37512 1948 99.77 0.21265 0.20969 0.2208 0.26836 0.2764 RANDOM 28.639
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] -1.89 6.14 -4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.785 r_dihedral_angle_4_deg 16.65 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_1_deg 7.594 r_long_range_B_refined 4.294 r_long_range_B_other 4.265 r_mcangle_it 2.805 r_mcangle_other 2.805 r_scangle_other 2.75 r_mcbond_it 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.785 r_dihedral_angle_4_deg 16.65 r_dihedral_angle_3_deg 13.813 r_dihedral_angle_1_deg 7.594 r_long_range_B_refined 4.294 r_long_range_B_other 4.265 r_mcangle_it 2.805 r_mcangle_other 2.805 r_scangle_other 2.75 r_mcbond_it 1.84 r_mcbond_other 1.84 r_scbond_it 1.804 r_scbond_other 1.804 r_angle_refined_deg 1.658 r_angle_other_deg 1.023 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5538 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing