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Crystal structures of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP and Oxalate
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 7.2 290 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.23 61.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.516 α = 90 b = 128.133 β = 90.03 c = 204.361 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 100 CCD MAR CCD 165 mm mirrors 2007-12-08 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 3.4 82.48 96.2 0.21 6.5 2.9 106471 36748 3.4 3.4 54.14
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) 3.4 3.58 98.5 0.52 2.1 3 5452
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 3.4 41.18 34917 1831 96.06 0.25243 0.25052 0.2328 0.28951 0.2706 RANDOM 53.828
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] -1.12 0.64 8.06 -6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_3_deg 16.352 r_dihedral_angle_4_deg 14.926 r_scangle_it 6.822 r_dihedral_angle_1_deg 4.756 r_scbond_it 3.687 r_mcangle_it 2.377 r_mcbond_it 1.151 r_angle_refined_deg 1.009 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_3_deg 16.352 r_dihedral_angle_4_deg 14.926 r_scangle_it 6.822 r_dihedral_angle_1_deg 4.756 r_scbond_it 3.687 r_mcangle_it 2.377 r_mcbond_it 1.151 r_angle_refined_deg 1.009 r_nbtor_refined 0.3 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.189 r_symmetry_hbond_refined 0.117 r_xyhbond_nbd_refined 0.111 r_metal_ion_refined 0.102 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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 14988 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 158
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement SCALA data scaling