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Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate
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
Crystal Properties Matthews coefficient Solvent content 3.32 63.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.011 α = 90 b = 127.011 β = 90 c = 144.652 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 315r 2016-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 2.62 63.51 100 10.6 5.5 78513
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 2.62 2.67 100 2.2 5.5
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 2.62 63.51 74461 4011 99.95 0.17562 0.1734 0.1811 0.21784 0.2213 RANDOM 68.639
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] 1.81 0.9 1.81 -5.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.177 r_dihedral_angle_4_deg 22.034 r_dihedral_angle_3_deg 19.867 r_long_range_B_refined 9.497 r_long_range_B_other 9.479 r_scangle_other 5.664 r_dihedral_angle_1_deg 5.446 r_mcangle_it 4.826 r_mcangle_other 4.826 r_scbond_it 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.177 r_dihedral_angle_4_deg 22.034 r_dihedral_angle_3_deg 19.867 r_long_range_B_refined 9.497 r_long_range_B_other 9.479 r_scangle_other 5.664 r_dihedral_angle_1_deg 5.446 r_mcangle_it 4.826 r_mcangle_other 4.826 r_scbond_it 3.67 r_scbond_other 3.651 r_mcbond_it 3.094 r_mcbond_other 3.091 r_angle_refined_deg 1.181 r_angle_other_deg 0.651 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 14008 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing