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Plasmodium falciparum pyruvate kinase complexed with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z4M D_1292121472
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MES, pH 6.5, 50 mM KCl, 10 mM MgCl2 and 14-24% PEG 600
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.89 α = 90 b = 112.4 β = 90 c = 131.97 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 PIXEL DECTRIS PILATUS 6M 2019-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.8 36.2 97.59 0.0597 0.999 10.6 3.3 53978 35.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 0.511
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292121472 1.8 36.2 1.34 53959 3237 97.61 0.2073 0.205 0.2052 0.2447 0.2444 42.17
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 f_dihedral_angle_d 28.4502 f_angle_d 1.3529 f_chiral_restr 0.078 f_bond_d 0.0144 f_plane_restr 0.0104
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3766 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing