6U2S

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LKFPDB entry 1LKF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529810 mg/mL protein in 10 mM fos-choline 14, 30 mM beta-OG, 10 mM sodium acetate, pH 5.4 against reservoir solution of 28% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8256.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.202α = 90
b = 37.769β = 119.8
c = 77.914γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.977CHESSF1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.567.6197.80.0540.9899.73.259415
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5384.70.270.9614.43

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 REPLACEMENTTHROUGHOUTPDB entry 1LKF1.567.6156377303897.720.16360.16230.1883RANDOM29.138
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]
-0.08-0.373.56-1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.914
r_dihedral_angle_4_deg14.277
r_dihedral_angle_3_deg11.324
r_dihedral_angle_1_deg6.806
r_angle_refined_deg1.884
r_angle_other_deg0.992
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.914
r_dihedral_angle_4_deg14.277
r_dihedral_angle_3_deg11.324
r_dihedral_angle_1_deg6.806
r_angle_refined_deg1.884
r_angle_other_deg0.992
r_chiral_restr0.126
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2386
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing