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Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in the orthorhombic apoform at 2.6 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HG4 PDB ID 2HG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 293 0.1M KH2PO4/K2HPO4, 1.3M ammonium sulfate, 10mM malonate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.659 α = 90 b = 119.806 β = 90 c = 50.162 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 100 CCD ADSC QUANTUM 315r 2007-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4
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 2.6 45 99.6 0.106 3.8 20741 20741 43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 99.9 0.368 1.6
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 (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 ID 2HG4 2.6 42.57 19692 19692 1016 99.37 0.19036 0.19036 0.18671 0.1858 0.26392 0.2529 RANDOM 27.284
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] -1.17 -1.1 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_4_deg 19.845 r_dihedral_angle_3_deg 19.552 r_dihedral_angle_1_deg 7.373 r_scangle_it 5.222 r_scbond_it 3.224 r_angle_refined_deg 2.147 r_mcangle_it 2.111 r_mcbond_it 1.141 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_4_deg 19.845 r_dihedral_angle_3_deg 19.552 r_dihedral_angle_1_deg 7.373 r_scangle_it 5.222 r_scbond_it 3.224 r_angle_refined_deg 2.147 r_mcangle_it 2.111 r_mcbond_it 1.141 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 3527 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 50
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling