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Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80.
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 4.03 69.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.053 α = 90 b = 127.495 β = 116.19 c = 118.168 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 2.85 86.08 100 0.083 0.094 11.8 4.6 181103 39558 2.85 2.85 77.4
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 2.85 2.93 100 0.541 0.612 2.5 4.5 2880
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 2.85 86.08 37465 1979 100 0.23699 0.23541 0.2338 0.26709 0.263 RANDOM 72.567
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] 0.4 -0.32 0.04 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_4_deg 11.965 r_dihedral_angle_1_deg 4.4 r_scangle_it 0.91 r_angle_refined_deg 0.873 r_scbond_it 0.478 r_mcangle_it 0.473 r_mcbond_it 0.254 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_3_deg 15.196 r_dihedral_angle_4_deg 11.965 r_dihedral_angle_1_deg 4.4 r_scangle_it 0.91 r_angle_refined_deg 0.873 r_scbond_it 0.478 r_mcangle_it 0.473 r_mcbond_it 0.254 r_chiral_restr 0.057 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 6745 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement