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Crystal of pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, soaked with allosteric activators AMP and Glucose 6-Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WRP
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 ATP, 5 mM AMP, 5 mM D-glucose 6-phosphate
Crystal Properties Matthews coefficient Solvent content 3.16 61.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.37 α = 90 b = 124.37 β = 90 c = 144.192 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 CCD ADSC QUANTUM 210r 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 53.85 100 8.3 5.5 97539
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.9 1.6 5.1
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 5WRP 2.4 53.85 92706 4790 99.96 0.18162 0.1793 0.148 0.22696 0.1944 RANDOM 27.566
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] 10.11 10.11 -20.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.666 r_dihedral_angle_4_deg 20.432 r_dihedral_angle_3_deg 17.274 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 2.773 r_long_range_B_other 2.771 r_mcangle_it 2.115 r_mcangle_other 2.114 r_scangle_other 2.088 r_scbond_it 1.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.666 r_dihedral_angle_4_deg 20.432 r_dihedral_angle_3_deg 17.274 r_dihedral_angle_1_deg 6.659 r_long_range_B_refined 2.773 r_long_range_B_other 2.771 r_mcangle_it 2.115 r_mcangle_other 2.114 r_scangle_other 2.088 r_scbond_it 1.589 r_scbond_other 1.583 r_mcbond_it 1.579 r_mcbond_other 1.579 r_angle_refined_deg 1.528 r_angle_other_deg 0.714 r_chiral_restr 0.099 r_bond_refined_d 0.014 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 335 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing