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Medium Resolution structure of the C-terminal family 65 Carbohydrate Binding Module (CBM65B) of endoglucanase Cel5A from Eubacterium cellulosolvens with a bound xyloglucan heptasaccharide (XXXG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BA6 PDB ENTRY 4BA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30%(W/V) PEG 4000 CO-CRYSTALLISED WITH 10 MM OF HEPTASACCHARIDE XXXG CRYOPROTECTAN WAS 30% GLYCEROL ADDED TO ABOVE CRYSTALLISATION BUFFER
Crystal Properties Matthews coefficient Solvent content 3.58 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.96 α = 90 b = 58.96 β = 90 c = 117.1 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.6 58.96 96.6 0.27 2.5 3.7 6535
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 2.6 2.74 97.2 1.5 0.6 3.9
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 4BA6 2.6 52.66 6206 303 95.3 0.25122 0.24861 0.253 0.30613 0.2672 RANDOM 71.468
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 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.556 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 6.178 r_mcangle_it 1.768 r_scbond_it 1.32 r_dihedral_angle_4_deg 1.238 r_angle_refined_deg 1.112 r_mcbond_other 0.962 r_mcbond_it 0.96 r_angle_other_deg 0.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.556 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_1_deg 6.178 r_mcangle_it 1.768 r_scbond_it 1.32 r_dihedral_angle_4_deg 1.238 r_angle_refined_deg 1.112 r_mcbond_other 0.962 r_mcbond_it 0.96 r_angle_other_deg 0.645 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it 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 977 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing