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Crystal structure of pyruvate kinase from Leishmania mexicana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKL PDB entry 1PKL, chain G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 277 20% Saturated ammonium sulphate, 100mM Na citrate, pH 4.2 (soaked in 40% Saturated ammonium sulphate, 100mM NaCl, pH 4.2), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.45 72.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.551 α = 90 b = 184.551 β = 90 c = 184.551 γ = 90
Symmetry Space Group P 42 3 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 4 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 3.1 40.3 99.5 0.042 0.042 11.9 8 19992
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 3.1 3.27 0.378 0.378 2.1 8
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-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, chain G 3.1 40.26 19964 995 99.3 0.215 0.207 0.246 0.2338 RANDOM 102.38
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_3_deg 19.168 r_dihedral_angle_4_deg 12.834 r_dihedral_angle_1_deg 5.412 r_scangle_it 1.669 r_angle_refined_deg 1.052 r_scbond_it 0.971 r_mcangle_it 0.763 r_mcbond_it 0.397 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.156 r_dihedral_angle_3_deg 19.168 r_dihedral_angle_4_deg 12.834 r_dihedral_angle_1_deg 5.412 r_scangle_it 1.669 r_angle_refined_deg 1.052 r_scbond_it 0.971 r_mcangle_it 0.763 r_mcbond_it 0.397 r_nbtor_refined 0.298 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.068 r_bond_refined_d 0.006 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_refined 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 3698 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling