6T6P

Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) at 1.57 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52970.2 M NH4H2PO4 0.1 M Tris-HCl pH 8.5 50 %v/v MPD
Crystal Properties
Matthews coefficientSolvent content
2.4950.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.639α = 90
b = 94.358β = 90
c = 151.068γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MToroidal mirrors2016-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97626ESRFID23-1

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
11.5780.03960.0530.070.0450.99711.63.913726812.6
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)
11.571.669.20.3050.4180.2840.8452.1

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 REPLACEMENTTHROUGHOUT4JRO1.5780.03130321685995.80.15190.15090.1702RANDOM17.321
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]
-0.480.64-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_4_deg17.917
r_dihedral_angle_3_deg11.521
r_dihedral_angle_1_deg5.659
r_angle_other_deg3.711
r_angle_refined_deg1.704
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_other0.012
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.2
r_dihedral_angle_4_deg17.917
r_dihedral_angle_3_deg11.521
r_dihedral_angle_1_deg5.659
r_angle_other_deg3.711
r_angle_refined_deg1.704
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_other0.012
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7168
Nucleic Acid Atoms
Solvent Atoms658
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing