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CBM29-2 mutant D83A complexed with mannohexaose: Probing the Mechanism of Ligand Recognition by Family 29 Carbohydrate Binding Modules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GWM PDB ENTRY 1GWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.5 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE PH6.5 10 MM MANNOHEXAOSE 25% GLYCEROL, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.2 0.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.15 α = 90 b = 42.636 β = 93.71 c = 60.182 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.3 100 99.8 0.06 32.4 3.6 31892
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 1.3 1.32 98.1 0.23 6.6 2.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GWM 1.3 30 30250 1610 99.8 0.162 0.161 0.175 RANDOM 8.66
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] 0.12 -0.01 0.11 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 17.839 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 7.334 r_scangle_it 3.801 r_angle_other_deg 3.35 r_scbond_it 2.658 r_angle_refined_deg 1.908 r_mcangle_it 1.739 r_mcbond_it 1.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.74 r_dihedral_angle_4_deg 17.839 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 7.334 r_scangle_it 3.801 r_angle_other_deg 3.35 r_scbond_it 2.658 r_angle_refined_deg 1.908 r_mcangle_it 1.739 r_mcbond_it 1.436 r_symmetry_vdw_refined 0.47 r_symmetry_vdw_other 0.37 r_nbd_other 0.192 r_nbd_refined 0.189 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.107 r_nbtor_other 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 1106 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing