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Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytic MCSG1, condition H5: 20% PEG 3350, 200mM KCl; AcbaC.18002.a.B1.PS02475 at 19.5mg/ml with 2mM of each AMPPNP, Glutamate, MgCl2, PPi; cryo: 20% EG with 2mM NAD/Mg; puck: exo0-1, tray: 266048 h5
Crystal Properties Matthews coefficient Solvent content 2.49 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.88 α = 90 b = 123.75 β = 110.93 c = 73.65 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+ Rigaku Varimax 2016-05-25 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) 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 2.1 50 99.3 0.099 0.996 10.83 3.7 69741 -3 24.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 98 0.54 2.58
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 4f4h 2.1 41.242 1.34 69703 2060 99.49 0.1663 0.165 0.1661 0.2103 0.2114 RANDOM 33.9518
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 15.284 f_angle_d 0.898 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8096 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 64
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction PHENIX model building PHENIX refinement Coot model building