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Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other iodide soak
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 native crystal: JCSG+ g10 30% PEG 2000 MME, 150mM KBr; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2; cryo: 20% EG, 5mM Mg/AMPPNP; tray 263060g10, puck ute6-5;
iodide crystal: JCSG+ b2: 20% PEG 3350, 200mM NaSCN; AnphA.17905.a.B1.PW37686 at 25mg/ml, 6mM each MgCl2, AMPPNP; cryo: soak in 10% and 20% of a 2.5M NaI solution in EG added to reservoir solution, 10 sec soaks each; tray 263060b2, puck hmh9-1
Crystal Properties Matthews coefficient Solvent content 2.14 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.14 α = 90 b = 93.76 β = 90 c = 72.49 γ = 90
Symmetry Space Group P 21 21 2
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 RIGAKU SATURN 944+ 2015-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (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 1.75 50 99.8 0.051 0.052 33.71 14.23 60460 -3 17.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.9 0.577 0.617 3.87 8.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD FREE R-VALUE iodide soak 1.75 47.905 1.99 60437 3078 99.79 0.1606 0.1589 0.1609 0.1936 0.1957 Random selection 24.0567
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.181 f_angle_d 1.016 f_chiral_restr 0.049 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4424 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing ARP model building Coot model building PHENIX refinement PDB_EXTRACT data extraction