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Structure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with cellobiose at 1.75 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other COMPLEX WITH SDP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 10 % PEG 4K, 100 MM NA ACETATE PH 4.6, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF FLUORESCEINYL DERIVED 1-BETA-METHYL-CELLOTRIOSIDE-THIO-GLUCOSIDE FOR 1 HOUR PRIOR CRYSTALLISATION. 30% PEG400 WAS ADDED AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.03 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.605 α = 90 b = 93.095 β = 90 c = 46.667 γ = 90
Symmetry Space Group P 21 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 120 CCD ADSC CCD 2003-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.75 20 99.4 0.11 14.7 5.3 27513 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 1.75 1.81 100 0.43 3.8 5
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 COMPLEX WITH SDP5 1.75 19.8 26134 1378 99.1 0.144 0.142 0.1586 0.181 0.1965 RANDOM 10.28
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] -0.09 -0.15 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.602 r_scangle_it 3.986 r_scbond_it 2.49 r_angle_refined_deg 1.507 r_mcangle_it 1.482 r_angle_other_deg 0.874 r_mcbond_it 0.846 r_nbd_other 0.262 r_symmetry_vdw_other 0.256 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.602 r_scangle_it 3.986 r_scbond_it 2.49 r_angle_refined_deg 1.507 r_mcangle_it 1.482 r_angle_other_deg 0.874 r_mcbond_it 0.846 r_nbd_other 0.262 r_symmetry_vdw_other 0.256 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.087 r_nbtor_other 0.085 r_symmetry_vdw_refined 0.074 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 2144 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling