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Crystal structure of S. aureus Pyruvate Kinase in complex with a naturally occurring bis-indole alkaloid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SITTING DROP 8.5 293 15-20% PEG3350, 0.4 M sodium malonate, 0.1 M bicine, pH 8.5, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.77 67.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.96 α = 86.05 b = 111.91 β = 72.14 c = 112.03 γ = 80.88
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 MARMOSAIC 225 mm CCD mirrors 2009-08-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 110.47 93.4 0.059 10.2 3.1 53839 53839
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 3.3 3.48 90.1 0.689 0.689 1.1 2.9 7594
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.3 60 53838 2729 93.43 0.1998 0.1983 0.2022 0.2259 0.2296 RANDOM 146.8076
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] 2.38 -1.28 -1.19 0.83 -3.16 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_3_deg 15.504 r_dihedral_angle_4_deg 14.229 r_dihedral_angle_1_deg 6.29 r_angle_refined_deg 1.413 r_angle_other_deg 0.925 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_3_deg 15.504 r_dihedral_angle_4_deg 14.229 r_dihedral_angle_1_deg 6.29 r_angle_refined_deg 1.413 r_angle_other_deg 0.925 r_chiral_restr 0.067 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17628 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 74
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MxDC data collection