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Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Molecular Dimensions Morpheus E5: 30mM each: Diethylene glycol, Triethylene-glycol, Tetraethylene glycol, Pentaethylene glycol; 100mM Imidazole, MES monohydrate (acid); 20% v/v PEG 500 MME; 10% w/v PEG 20000; AnphA.17905.a.B1.PW37686 at 30mg/ml, 5mM each MgCl2, ADO and TPP; cryo: direct; tray 264490e5, puck ute6-11
Crystal Properties Matthews coefficient Solvent content 2.29 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.75 α = 90 b = 117.12 β = 108.57 c = 55.89 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 100 CCD RIGAKU SATURN 944+ 2015-06-22 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 1.55 50 99.5 0.062 0.064 24.47 11.1 89068 -3 10.94
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 1.55 1.59 94.8 0.376 0.427 3.55 4.2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5cc8 1.55 44.501 1.35 89030 2021 99.57 0.1425 0.1419 0.1425 0.1674 0.1691 17.9481
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 11.29 f_angle_d 1.085 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4619 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 118
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing Coot model building PHENIX refinement