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Structure of the CBM22-2 xylan-binding domain in complex with 1,3:1,4 Beta-glucotetraose B from Paenibacillus barcinonensis Xyn10C
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 6 293 1.85M Sodium malonate.
Ratio protein/precipitant=0.5/1
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.478 α = 90 b = 92.478 β = 90 c = 48.382 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 2013-10-18 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 1.8 48.38 100 0.092 0.032 14.8 9.2 42863 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 1.8 1.9 100 0.432 4.6 8.8
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 1.8 48.38 40685 2161 99.98 0.20525 0.20416 0.2109 0.22572 0.2334 RANDOM 24.026
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] -0.23 -0.12 -0.23 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.896 r_dihedral_angle_4_deg 26.516 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 6.249 r_long_range_B_other 5.632 r_long_range_B_refined 5.627 r_scangle_other 3.83 r_mcangle_it 2.843 r_mcangle_other 2.843 r_scbond_it 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.896 r_dihedral_angle_4_deg 26.516 r_dihedral_angle_3_deg 14.131 r_dihedral_angle_1_deg 6.249 r_long_range_B_other 5.632 r_long_range_B_refined 5.627 r_scangle_other 3.83 r_mcangle_it 2.843 r_mcangle_other 2.843 r_scbond_it 2.39 r_scbond_other 2.389 r_mcbond_it 1.779 r_mcbond_other 1.777 r_angle_refined_deg 1.492 r_angle_other_deg 1.225 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 113 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing