6T5X

Crystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AFN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 10 mM NADPH (added to the protein solution) Cryoprotection of the crystals: dipping them in 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 26% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.1843.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.43α = 90
b = 71.144β = 94.42
c = 81.366γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6Mtoroidal mirror2016-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.558.4995.90.0250.0320.020.99918.32.3673422.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5397.40.3870.4910.3350.8432.52.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4AFN1.558.2163956343495.690.16020.15880.185RANDOM25.223
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]
0.39-0.341.15-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg14.5
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg5.612
r_angle_refined_deg1.479
r_angle_other_deg0.934
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg14.5
r_dihedral_angle_3_deg13.385
r_dihedral_angle_1_deg5.612
r_angle_refined_deg1.479
r_angle_other_deg0.934
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3554
Nucleic Acid Atoms
Solvent Atoms456
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing