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Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii in non-covalent complex with pyridoxal phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YL5 PDB entry 4yl5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Microlytics MGSC1 screen, c8: 25% PEG 4000, 200mM ammonium citrate, 100mM Na citrate/HCl, pH 5.6; AcbaC.00867.a.B1.PW37632 at 22 mg/ml; crystal soaked for 2h in reservoir solution with 5mM Pyridoxal phosphate, tray 261062, puck hml12-2; cryo: 20% EG
Crystal Properties Matthews coefficient Solvent content 2.55 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.82 α = 90 b = 108.1 β = 90 c = 88.88 γ = 90
Symmetry Space Group C 2 2 21
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+ 2015-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.6 98.1 0.044 0.046 1 45 37353 -3 14.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 78.8 0.487 0.602 0.736 2.23
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 PDB entry 4yl5 1.65 46.181 1.34 34354 1802 99.69 0.1579 0.1569 0.1582 0.1761 0.1777 Random selection 21.1937
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 15.62 f_angle_d 0.838 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1631 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building PDB_EXTRACT data extraction