4ZJU

Structure of a NADH-dependent enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NQZPDB entry 4NQZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290Molecular Dimensions Morpheus screen, h12: Morpheus H12: 20mM each L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic); 100mM Tris (base)/Bicine pH 8.5; 15% each MPD (racemic), PEG 1000, PEG 3350; AcbaC.00170.a.B1.PW37673 at 25mg/ml with 5mM NADH; tray 262582, puck oxi7-1
Crystal Properties
Matthews coefficientSolvent content
2.652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.02α = 90
b = 92.44β = 90
c = 93.83γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.25099.90.0490.05518.714.896282-39.45
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)RedundancyNumber Unique Reflections (All)
11.21.231000.5370.6072.754.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 4NQZ1.246.9151.3496277201599.940.12520.12480.142Random selection15.1289
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.665
f_angle_d1.269
f_chiral_restr0.072
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1941
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms45

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
ARPmodel building
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction