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Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with benzothiazole-2,5-disulfonic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.554 α = 90 b = 131.282 β = 90 c = 167.602 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.45 44.41 100 0.095 0.102 16.1 7.3 360184 49123 2.45 2.45 52.1
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 2.45 2.58 100 0.563 0.605 4.1 7.5 7089
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PKL 2.45 44.41 46606 2485 99.9 0.23608 0.23448 0.26576 0.2716 RANDOM 52.196
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] -1.13 3.92 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_4_deg 16.723 r_dihedral_angle_3_deg 16.33 r_dihedral_angle_1_deg 5.672 r_scangle_it 2.448 r_scbond_it 1.401 r_angle_refined_deg 1.259 r_mcangle_it 1.019 r_mcbond_it 0.536 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_4_deg 16.723 r_dihedral_angle_3_deg 16.33 r_dihedral_angle_1_deg 5.672 r_scangle_it 2.448 r_scbond_it 1.401 r_angle_refined_deg 1.259 r_mcangle_it 1.019 r_mcbond_it 0.536 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 6748 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 54
Software Software Software Name Purpose DNA data collection REFMAC refinement MOSFLM data reduction SCALA data scaling