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Crystal structure of a beta-ketoacyl reductase FabG4 from Mycobacterium tuberculosis H37Rv complexed with NAD+ and Hexanoyl-CoA at 2.5 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6I PDB ENTRY 3Q6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 300 45% Polypropylene Glycol, 0.1M MES pH 6.5, 10mM Hexanoyl CoA, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.059 α = 90 b = 103.059 β = 90 c = 76.047 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 IMAGE PLATE RIGAKU RAXIS IV++ 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.497 89.252 98.8 0.103 18.9 7.5 16296 16296
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63 97.5 0.848 0.848 0.9 7.5
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 PDB ENTRY 3Q6I 2.5 89.25 15469 825 98.51 0.19208 0.1895 0.1878 0.24047 0.236 RANDOM 42.721
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] 0.55 0.28 0.55 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_4_deg 20.543 r_dihedral_angle_3_deg 18.501 r_dihedral_angle_1_deg 6.535 r_scangle_it 3.776 r_scbond_it 2.275 r_angle_refined_deg 1.79 r_mcangle_it 1.588 r_mcbond_it 0.861 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.536 r_dihedral_angle_4_deg 20.543 r_dihedral_angle_3_deg 18.501 r_dihedral_angle_1_deg 6.535 r_scangle_it 3.776 r_scbond_it 2.275 r_angle_refined_deg 1.79 r_mcangle_it 1.588 r_mcbond_it 0.861 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2986 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 108
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling