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Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP and thiamine-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytic MGCS G4 optimization screen: 19% PEG 3350, 200mM KNa-tartrate, 100mM HEPES/NaOH pH 7.75; AcbaC.17905.a.B1.PW37686 at 30mg/ml with 5mM MgCl2/ANP, then over night soak with in reservoir solution with 5mM MgCl2/ANP/TMP; cryo: soak solution with 20% EG; tray 264486e7, puck RUX3-7
Crystal Properties Matthews coefficient Solvent content 2.17 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.96 α = 90 b = 93.29 β = 90 c = 73.48 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 RAYONIX MX-225 2015-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.7 50 99.5 0.053 0.058 22.56 6.2 66411 66088 -3 18.91
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 1.7 1.74 99.2 0.587 0.64 3.43 6.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5d9u 1.7 39.41 1.34 66070 2015 99.5 0.1504 0.1495 0.1521 0.1769 0.1794 Random selection 26.7195
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 11.37 f_angle_d 0.837 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 128
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction