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Structure of a beta-1,3-glucan binding CBM6 from Bacillus halodurans
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 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.795 α = 108.95 b = 40.834 β = 105.93 c = 56.118 γ = 90
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 1.59 20 90.1 0.03 24.9 3.7 28471 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 1.59 1.65 68.5 0.17 5.7 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 1.59 20 28471 1517 90.1 0.119 0.117 0.1285 0.166 0.1504 RANDOM 13.68
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] 0.67 -0.03 -0.15 -0.37 -0.03 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.431 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_3_deg 10.454 r_dihedral_angle_1_deg 6.909 r_scangle_it 5.145 r_scbond_it 3.546 r_mcangle_it 2.416 r_mcbond_it 1.671 r_angle_refined_deg 1.615 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.431 r_dihedral_angle_4_deg 16.779 r_dihedral_angle_3_deg 10.454 r_dihedral_angle_1_deg 6.909 r_scangle_it 5.145 r_scbond_it 3.546 r_mcangle_it 2.416 r_mcbond_it 1.671 r_angle_refined_deg 1.615 r_angle_other_deg 0.826 r_symmetry_vdw_other 0.375 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.203 r_nbd_other 0.19 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.125 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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 350 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOLREP phasing