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Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKL PDB ENTRY 1PKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.31 62.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.486 α = 89.73 b = 151.14 β = 80.17 c = 160.319 γ = 71.64
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 MAR CCD 165 mm mirrors 2008-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 ESRF ID23-1
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 2.3 41.96 94.7 0.095 8.2 1.9 913876 470114 2.3 2.3 41.2
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 2.3 2.42 90.8 0.638 1.3 1.3 65953
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 1PKL 2.3 34.46 446260 23579 94.63 0.20111 0.19841 0.2006 0.25198 0.2529 RANDOM 42.789
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] -2.77 0.29 0.16 -0.41 -0.84 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.789 r_dihedral_angle_4_deg 16.527 r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 4.96 r_scangle_it 1.391 r_angle_refined_deg 1.106 r_scbond_it 0.87 r_mcangle_it 0.492 r_nbtor_refined 0.294 r_mcbond_it 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.789 r_dihedral_angle_4_deg 16.527 r_dihedral_angle_3_deg 16.234 r_dihedral_angle_1_deg 4.96 r_scangle_it 1.391 r_angle_refined_deg 1.106 r_scbond_it 0.87 r_mcangle_it 0.492 r_nbtor_refined 0.294 r_mcbond_it 0.254 r_metal_ion_refined 0.21 r_symmetry_vdw_refined 0.188 r_nbd_refined 0.182 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 60784 Nucleic Acid Atoms Solvent Atoms 4100 Heterogen Atoms 973
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement SCALA data scaling