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Structure of M2 pyruvate kinase in complex with phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJT PDB entry 3BJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 10-16% PEG 8000, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.6 α = 90 b = 139.35 β = 90.52 c = 111.28 γ = 90
Symmetry Space Group P 1 21 1
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 PSI PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.55 66.09 98.2 0.085 0.053 15.6 6.9 79477 2.55 2.55
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 2.55 2.62 93.6 0.633 0.757 2.6 6.5 36105
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 PDB entry 3BJT 2.55 51.67 75250 3978 100 0.21453 0.21243 0.2039 0.25376 0.2438 RANDOM 49.578
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] -0.16 -0.08 0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.104 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_4_deg 13.267 r_dihedral_angle_1_deg 4.122 r_angle_refined_deg 0.878 r_scangle_it 0.787 r_mcangle_it 0.437 r_scbond_it 0.431 r_mcbond_it 0.237 r_chiral_restr 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.104 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_4_deg 13.267 r_dihedral_angle_1_deg 4.122 r_angle_refined_deg 0.878 r_scangle_it 0.787 r_mcangle_it 0.437 r_scbond_it 0.431 r_mcbond_it 0.237 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15352 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement SCALA data scaling