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Structure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with glucose-isofagomine at 1.9 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 12 % PEG 4K, 12 % PEG 4K, 100 MM SODIUM ACTETATE PH 4.6, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF GLUCOSE-ISOFAGOMINE FOR 1 HOUR PRIOR CRYSTALLISATION. 30% PEG 400 ADDED AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.03 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.788 α = 90 b = 92.83 β = 90 c = 46.695 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 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2003-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.9 20 97.8 0.071 14.6 2.8 21248 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 1.9 1.97 95.1 0.206 4.9 2.9
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 COMPLEX WITH SDP5 1.9 19.8 20168 1079 97.8 0.134 0.132 0.1502 0.177 0.1898 RANDOM 11.27
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] 0.05 -0.16 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 3.346 r_scbond_it 2.103 r_angle_refined_deg 1.537 r_mcangle_it 1.164 r_angle_other_deg 1.06 r_mcbond_it 0.696 r_nbd_other 0.257 r_symmetry_vdw_other 0.252 r_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.546 r_scangle_it 3.346 r_scbond_it 2.103 r_angle_refined_deg 1.537 r_mcangle_it 1.164 r_angle_other_deg 1.06 r_mcbond_it 0.696 r_nbd_other 0.257 r_symmetry_vdw_other 0.252 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.097 r_symmetry_vdw_refined 0.093 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 2145 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling