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Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, ATP and allosteric activator AMP
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 13% 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
Crystal Properties Matthews coefficient Solvent content 3.32 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.19 α = 90 b = 127.19 β = 90 c = 144.924 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 2016-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
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 1.9 60.54 100 12 4.8 206700
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 1.9 1.93 100 3 4.3
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 1.9 60.54 195933 10685 99.98 0.19812 0.19676 0.2028 0.22292 0.229 RANDOM 36.261
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] 0.75 0.37 0.75 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.268 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 14.543 r_long_range_B_refined 6.15 r_long_range_B_other 6.15 r_dihedral_angle_1_deg 6.082 r_scangle_other 3.756 r_scbond_it 3.111 r_scbond_other 2.609 r_mcangle_other 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.268 r_dihedral_angle_4_deg 18.8 r_dihedral_angle_3_deg 14.543 r_long_range_B_refined 6.15 r_long_range_B_other 6.15 r_dihedral_angle_1_deg 6.082 r_scangle_other 3.756 r_scbond_it 3.111 r_scbond_other 2.609 r_mcangle_other 2.36 r_mcangle_it 2.359 r_mcbond_it 1.704 r_mcbond_other 1.702 r_angle_refined_deg 1.264 r_angle_other_deg 0.691 r_chiral_restr 0.088 r_bond_refined_d 0.012 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 1440 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing