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Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C in complex with xylotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1.95M Sodium malonate.
Ratio protein/precipitant=1/0.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.455 α = 90 b = 92.455 β = 90 c = 48.425 γ = 120
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-F 2013-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 48.42 99.9 0.09 0.031 17.5 9.3 33856 1 1
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 1.95 2.05 99.7 0.289 7.6 9 4948
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 4xun 1.95 48.42 32123 1715 99.95 0.1799 0.17814 0.1859 0.21251 0.2202 RANDOM 21.523
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] 0.22 0.11 0.22 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_4_deg 25.109 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 6.455 r_long_range_B_other 5.291 r_long_range_B_refined 5.29 r_scangle_other 3.958 r_mcangle_it 2.76 r_mcangle_other 2.76 r_scbond_it 2.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_4_deg 25.109 r_dihedral_angle_3_deg 13.293 r_dihedral_angle_1_deg 6.455 r_long_range_B_other 5.291 r_long_range_B_refined 5.29 r_scangle_other 3.958 r_mcangle_it 2.76 r_mcangle_other 2.76 r_scbond_it 2.644 r_scbond_other 2.644 r_mcbond_it 1.872 r_mcbond_other 1.868 r_angle_other_deg 1.668 r_angle_refined_deg 1.519 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_bond_other_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 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 3789 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing