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Structure of a beta-1,3-glucan binding CBM6 from Bacillus halodurans in complex with xylobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GMM PDB ENTRY 1GMM
Crystallization Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.711 α = 108.89 b = 40.967 β = 105.87 c = 56.039 γ = 90.03
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.62 20 91.9 0.05 14.9 3.6 27417 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 1.62 1.68 84.4 0.24 4.5 3.2
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 PDB ENTRY 1GMM 1.62 20 27417 1454 91.9 0.121 0.118 0.129 0.179 0.1495 RANDOM 15.12
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] 0.45 0.07 -0.26 0.04 0.21 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.019 r_dihedral_angle_4_deg 15.414 r_dihedral_angle_3_deg 10.708 r_dihedral_angle_1_deg 6.761 r_scangle_it 4.903 r_scbond_it 3.355 r_mcangle_it 2.295 r_angle_refined_deg 1.687 r_mcbond_it 1.594 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.019 r_dihedral_angle_4_deg 15.414 r_dihedral_angle_3_deg 10.708 r_dihedral_angle_1_deg 6.761 r_scangle_it 4.903 r_scbond_it 3.355 r_mcangle_it 2.295 r_angle_refined_deg 1.687 r_mcbond_it 1.594 r_angle_other_deg 0.835 r_symmetry_vdw_other 0.352 r_nbd_refined 0.309 r_symmetry_hbond_refined 0.235 r_nbd_other 0.193 r_xyhbond_nbd_refined 0.191 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.184 r_chiral_restr 0.117 r_nbtor_other 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement MOLREP phasing