6T77

Crystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) NADP-complex at 1.75 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q7B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22979.5 mg/ml protein solution mixed with NADP+ at 11.5 mM concentration Well solution: 0.1 M phosphate-citrate 4.2 pH 40 %v/v PEG 300
Crystal Properties
Matthews coefficientSolvent content
2.3948.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.723α = 90
b = 118.842β = 90
c = 119.759γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MToroidal mirrors2017-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.96862ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7559.8896.80.0340.0260.998153.84796627.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7899.30.380.2970.86123.8

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 REPLACEMENTTHROUGHOUT1Q7B1.7559.8845483244996.40.15960.15790.1938RANDOM38.978
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]
2.4-1.82-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.331
r_dihedral_angle_4_deg15.683
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg5.703
r_angle_other_deg3.738
r_angle_refined_deg1.853
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_other0.013
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.331
r_dihedral_angle_4_deg15.683
r_dihedral_angle_3_deg13.766
r_dihedral_angle_1_deg5.703
r_angle_other_deg3.738
r_angle_refined_deg1.853
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_other0.013
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3568
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing