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Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DYO
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 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.539 α = 90 b = 92.539 β = 90 c = 48.401 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 1.75 33.45 100 0.094 0.043 5.8 5.8 46784 1 1 12.643
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 1.75 1.84 100 0.403 1.9 5.8 6810
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1dyo 1.75 33.45 44391 2375 99.99 0.15295 0.15144 0.182 0.231 RANDOM 17.693
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 24.357 r_dihedral_angle_3_deg 13.162 r_dihedral_angle_1_deg 6.238 r_long_range_B_refined 4.574 r_long_range_B_other 4.498 r_scangle_other 3.032 r_mcangle_it 2.168 r_mcangle_other 2.167 r_scbond_it 1.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 24.357 r_dihedral_angle_3_deg 13.162 r_dihedral_angle_1_deg 6.238 r_long_range_B_refined 4.574 r_long_range_B_other 4.498 r_scangle_other 3.032 r_mcangle_it 2.168 r_mcangle_other 2.167 r_scbond_it 1.948 r_scbond_other 1.947 r_angle_refined_deg 1.451 r_mcbond_it 1.372 r_mcbond_other 1.369 r_angle_other_deg 1.199 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 231 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing