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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 1B57 Homology model derived from PDB ENTRY 1B57
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 4.07 69.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.285 α = 90 b = 120.227 β = 90 c = 164.823 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 225 mm CCD 2008-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 1.51 97.1 96.5 91761 91761
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.51 1.56 89.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Homology model derived from PDB ENTRY 1B57 1.51 97.1 91755 91755 4602 95.99 0.16674 0.16623 0.17637 0.2509 RANDOM 22.063
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] 0.79 -0.5 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 18.553 r_dihedral_angle_3_deg 11.39 r_dihedral_angle_1_deg 9.437 r_scangle_it 2.361 r_scbond_it 1.473 r_angle_refined_deg 1.21 r_mcangle_it 0.741 r_mcbond_it 0.42 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 18.553 r_dihedral_angle_3_deg 11.39 r_dihedral_angle_1_deg 9.437 r_scangle_it 2.361 r_scbond_it 1.473 r_angle_refined_deg 1.21 r_mcangle_it 0.741 r_mcbond_it 0.42 r_nbtor_refined 0.305 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.086 r_metal_ion_refined 0.046 r_bond_refined_d 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 23
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling