Navigation Tabs Ambient temperature structure of Bifidobacterium longum phosphoketolase with thiamine diphosphate
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 Equal amount of 15 mg ml-1 PKT solution (4 mM DTT, 10 mg ml-1 ThDpp) and precipitant solution (50 mM malonate, 12% tacsimate (pH5), 17% PEG3350) were mixed in order to prepare seed crystals. Preparations of seed crystals of PKT were performed by utilizing light induced crystallization method which promoted to form initial crystal nucleus by evanescent field arised from light irradiation to gold nano-particle vapored on general polystyrene plate (Fujifilm Wako). After 16 h, precipitated crystals were homogenized and centrifuged to use supernatant as seed solution. For the purpose of forming micro-sized crystals of PKT, 1176 micro l of protein-precipitant solution mixture as the same components of seed crystals preparation was mixed with 120 micro l of the seed solution in a 1.5 ml tube. After gentle rotation at 25 degree C for 2 h, the supernatant was exchanged to the same precipitant solution. The same buffer exchange was iteratively conducted after 10 h and 16 h.
Crystal Properties Matthews coefficient Solvent content 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.62 α = 90 b = 185.8 β = 99.61 c = 162.89 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 293 CCD MPCCD 2016-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.7714 SACLA BL3
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.5 46.8 100 0.938 0.215 3.64 234 292114 57.854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 100 0.493 1.006 1.11 165.2
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 3AI7 2.5 46.8 277500 14633 99.98 0.1642 0.1613 0.17 0.2176 0.22 RANDOM 54.255
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] -0.9 -0.48 -1 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 18.65 r_dihedral_angle_3_deg 17.076 r_dihedral_angle_1_deg 7.56 r_angle_refined_deg 1.582 r_angle_other_deg 1.277 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 18.65 r_dihedral_angle_3_deg 17.076 r_dihedral_angle_1_deg 7.56 r_angle_refined_deg 1.582 r_angle_other_deg 1.277 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51353 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement Cheetah data collection CrystFEL data processing MOLREP phasing Coot model building CrystFEL data reduction CrystFEL data scaling
