☰ Navigation Tabs
Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.
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 EVAPORATION 7.2 277 7 12 % PEG 8,000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10% glycerol, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.77 α = 90 b = 129.48 β = 90 c = 165.75 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 315 mirrors 2008-12-11 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 2.35 49.57 98 0.058 0.024 22 6.5 54542 2.35 2.35 44.2
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 2.35 2.48 98 0.352 0.146 4.5 6.5 7772
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2.35 44.73 54537 51776 2761 98.01 0.19342 0.19144 0.2079 0.23119 0.247 RANDOM 70.735
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] 0.04 0.15 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 17.9 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 5.443 r_scangle_it 2.145 r_scbond_it 1.235 r_angle_refined_deg 1.124 r_mcangle_it 0.848 r_mcbond_it 0.439 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 17.9 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 5.443 r_scangle_it 2.145 r_scbond_it 1.235 r_angle_refined_deg 1.124 r_mcangle_it 0.848 r_mcbond_it 0.439 r_chiral_restr 0.078 r_bond_refined_d 0.008 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 7519 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 89
Software Software Software Name Purpose ADSC data collection REFMAC refinement MOSFLM data reduction SCALA data scaling