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Apo crystal structure of Leishmania mexicana(LmPYK)pyruvate kinase
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 10-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.579 α = 90 b = 167.333 β = 90 c = 132.199 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 MAR CCD 165 mm mirrors 2008-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 2 52.13 99.8 0.099 15.2 7.2 89910 2 2 30.2
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) 1 2 2.11 100 0.588 3 7.3 13071
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 2 39.32 85394 4504 99.7 0.17064 0.16863 0.1843 0.20906 0.2272 RANDOM 25.8
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] 0.05 -0.41 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.592 r_dihedral_angle_4_deg 22.089 r_dihedral_angle_3_deg 15.957 r_scangle_it 6.457 r_dihedral_angle_1_deg 6.264 r_scbond_it 4.036 r_mcangle_it 2.225 r_angle_refined_deg 2.052 r_mcbond_it 1.313 r_chiral_restr 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.592 r_dihedral_angle_4_deg 22.089 r_dihedral_angle_3_deg 15.957 r_scangle_it 6.457 r_dihedral_angle_1_deg 6.264 r_scbond_it 4.036 r_mcangle_it 2.225 r_angle_refined_deg 2.052 r_mcbond_it 1.313 r_chiral_restr 0.181 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 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 7512 Nucleic Acid Atoms Solvent Atoms 734 Heterogen Atoms 32
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement SCALA data scaling