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Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with ponceau S and acid blue 25.
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 3.82 67.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.109 α = 90 b = 164.798 β = 115.8 c = 123.348 γ = 90
Symmetry Space Group C 1 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 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 2.7 21.14 100 0.123 0.144 10.2 3.7 89354 2.7 2.7 56.4
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 2.7 2.85 100 0.542 0.64 2.1 3.5 12910
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 1PKL 2.7 21.14 84872 4480 99.77 0.21677 0.21535 0.2149 0.24414 0.2429 RANDOM 45.246
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] 0.39 0.44 -0.23 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.249 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_4_deg 14.023 r_dihedral_angle_1_deg 4.233 r_angle_refined_deg 0.859 r_scangle_it 0.749 r_mcangle_it 0.428 r_scbond_it 0.4 r_mcbond_it 0.232 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.249 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_4_deg 14.023 r_dihedral_angle_1_deg 4.233 r_angle_refined_deg 0.859 r_scangle_it 0.749 r_mcangle_it 0.428 r_scbond_it 0.4 r_mcbond_it 0.232 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 13572 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement