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Crystal structure of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, AMP and inhibitor Ribose 5-Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM AMP, 5 mM D-ribose 5-phosphate
Crystal Properties Matthews coefficient Solvent content 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.55 α = 90 b = 125.55 β = 90 c = 143.821 γ = 120
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 2M-F 2016-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
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 2.55 62.77 100 0.124 8.8 4 82657 38.9
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 2.55 2.6 100 0.94 1.6 4.1
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 5WSC 2.55 62.77 78503 4106 99.96 0.20773 0.20567 0.2083 0.24762 0.2462 RANDOM 54.418
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] 1.36 0.68 1.36 -4.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.22 r_dihedral_angle_3_deg 19.41 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_1_deg 7.185 r_long_range_B_refined 5.633 r_long_range_B_other 5.632 r_scangle_other 2.677 r_mcangle_other 2.59 r_mcangle_it 2.589 r_scbond_it 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.22 r_dihedral_angle_3_deg 19.41 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_1_deg 7.185 r_long_range_B_refined 5.633 r_long_range_B_other 5.632 r_scangle_other 2.677 r_mcangle_other 2.59 r_mcangle_it 2.589 r_scbond_it 1.64 r_scbond_other 1.64 r_mcbond_it 1.574 r_mcbond_other 1.573 r_angle_refined_deg 1.219 r_angle_other_deg 1.16 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14172 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing