☰ Navigation Tabs
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 3350, 100 mM sodium Cacodylate, 50 mM MgCl2, 100 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 46.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.26 α = 90 b = 70.6 β = 105.72 c = 167.6 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 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.9 80.7 90.3 0.167 0.189 7.5 4.3 44252 2.9 2.9 50.2
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 2.9 3.06 90 0.627 0.7 2.2 4.3 27597
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 2.9 56.14 41633 2211 89.39 0.24823 0.24562 0.2402 0.2972 0.2935 RANDOM 43.122
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] 0.86 -0.76 -0.15 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.865 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_4_deg 13.375 r_dihedral_angle_1_deg 3.539 r_angle_refined_deg 0.773 r_mcangle_it 0.231 r_mcbond_it 0.129 r_scangle_it 0.114 r_scbond_it 0.062 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.865 r_dihedral_angle_3_deg 13.788 r_dihedral_angle_4_deg 13.375 r_dihedral_angle_1_deg 3.539 r_angle_refined_deg 0.773 r_mcangle_it 0.231 r_mcbond_it 0.129 r_scangle_it 0.114 r_scbond_it 0.062 r_chiral_restr 0.047 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 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 14721 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement SCALA data scaling