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Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with 1,3,6,8-pyrenetetrasulfonic acid
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 12-16 % Peg 8,000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.02 59.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.86 α = 90 b = 129.86 β = 90 c = 165.2 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 100 CCD ADSC QUANTUM 315r mirrors 2008-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
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 2.1 20.69 99.9 0.076 0.08 20.1 9 76957 76957 2.1 2.1 31.6
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 2.1 2.21 100 0.527 0.561 4.2 8.7 11124
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1PKL 2.1 20.69 2.1 2.1 76956 73091 3865 100 0.18821 0.18554 0.2388 0.2316 RANDOM 44.681
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] 0.37 2.39 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 20.132 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_1_deg 6.333 r_scangle_it 5.393 r_scbond_it 3.303 r_mcangle_it 2.008 r_angle_refined_deg 1.822 r_mcbond_it 1.156 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 20.132 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_1_deg 6.333 r_scangle_it 5.393 r_scbond_it 3.303 r_mcangle_it 2.008 r_angle_refined_deg 1.822 r_mcbond_it 1.156 r_chiral_restr 0.145 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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 7506 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALA data scaling