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Structural Characterization of tetrameric Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase - substrate binding and catalysis mechanism of a class IIa bacterial aldolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EKL PDB ENTRY 3EKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 26% PEG 300, 0.1 NaAcetate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.99 69.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.638 α = 90 b = 119.492 β = 90 c = 164.011 γ = 90
Symmetry Space Group I 2 2 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 CCD MARMOSAIC 300 mm CCD 2008-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.31 96.7 98.9 140514 140514
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.31 1.36 94.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3EKL 1.31 96.67 133473 133473 7033 98.74 0.16 0.16 0.15887 0.1588 0.16706 0.1668 RANDOM 22.716
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] 0.85 -0.38 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.41 r_dihedral_angle_4_deg 14.1 r_dihedral_angle_3_deg 11.487 r_dihedral_angle_1_deg 10.298 r_scangle_it 2.204 r_sphericity_free 2.055 r_sphericity_bonded 1.95 r_scbond_it 1.48 r_angle_refined_deg 1.171 r_mcangle_it 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.41 r_dihedral_angle_4_deg 14.1 r_dihedral_angle_3_deg 11.487 r_dihedral_angle_1_deg 10.298 r_scangle_it 2.204 r_sphericity_free 2.055 r_sphericity_bonded 1.95 r_scbond_it 1.48 r_angle_refined_deg 1.171 r_mcangle_it 0.9 r_rigid_bond_restr 0.766 r_mcbond_it 0.541 r_nbtor_refined 0.304 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.082 r_xyhbond_nbd_refined 0.081 r_metal_ion_refined 0.018 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2482 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 23
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling