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Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C in complex with xylotetraose
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 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.769 α = 90 b = 92.769 β = 90 c = 48.571 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 CCD MARMOSAIC 225 mm CCD 2013-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
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 1.67 33.55 100 0.091 0.042 13.1 5.6 54496 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 1.67 1.76 100 0.451 3.4 5.3 7920
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 1.67 33.55 51625 2850 99.98 0.15964 0.15779 0.1621 0.19366 0.1881 RANDOM 16.313
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] 0.54 0.54 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_4_deg 23.828 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 7.236 r_long_range_B_refined 3.411 r_long_range_B_other 3.393 r_scangle_other 1.958 r_mcangle_it 1.792 r_mcangle_other 1.792 r_angle_refined_deg 1.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.387 r_dihedral_angle_4_deg 23.828 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 7.236 r_long_range_B_refined 3.411 r_long_range_B_other 3.393 r_scangle_other 1.958 r_mcangle_it 1.792 r_mcangle_other 1.792 r_angle_refined_deg 1.622 r_angle_other_deg 1.622 r_scbond_it 1.488 r_scbond_other 1.488 r_mcbond_it 1.229 r_mcbond_other 1.228 r_chiral_restr 0.108 r_bond_other_d 0.023 r_bond_refined_d 0.019 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 94 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing