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Crystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1a)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GEV PDB ENTRY 2GEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 14.4% (W/V) PEG 8000, 20% (V/V) GLYCEROL, 0.08 M SODIUM CACODYLATE, PH 6.5, AND 0.16 M CALCIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 4.07 69.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.28 α = 90 b = 105.28 β = 90 c = 90.8 γ = 120
Symmetry Space Group P 31 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 110 CCD MARRESEARCH 2007-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.9 30 98.9 0.12 10.1 6 13018 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 2.9 3.06 99.5 0.49 3.3 6
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 2GEV 2.9 28.74 12375 639 98.32 0.19914 0.19675 0.1967 0.24488 0.2436 RANDOM 54.855
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 1.17 1.17 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_dihedral_angle_3_deg 21.036 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_1_deg 5.669 r_mcangle_it 4.926 r_scbond_it 3.915 r_mcbond_it 3.102 r_angle_refined_deg 1.479 r_chiral_restr 0.1 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.753 r_dihedral_angle_3_deg 21.036 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_1_deg 5.669 r_mcangle_it 4.926 r_scbond_it 3.915 r_mcbond_it 3.102 r_angle_refined_deg 1.479 r_chiral_restr 0.1 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_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_mcangle_other r_scbond_other r_scangle_it 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 2439 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing