4D44

Crystal structure of S. aureus FabI in complex with NADP and 5-ethyl- 4-fluoro-2-((2-fluoropyridin-3-yl)oxy)phenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ALKPDB ENTRY 4ALK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M NA/K-PHOSPHATE PH 6.5, 41% MPD
Crystal Properties
Matthews coefficientSolvent content
2.9257.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.97α = 98.06
b = 94.74β = 97.38
c = 94.8γ = 112.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.833.6497.50.0711.442542376
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.996.40.622.34

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 4ALK1.833.642414571277097.490.141840.140330.17029RANDOM28.788
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]
1.88-0.12-0.19-0.8-1-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg14.985
r_scangle_it6.415
r_dihedral_angle_1_deg6.11
r_scbond_it4.178
r_mcangle_it2.344
r_angle_refined_deg1.873
r_mcbond_it1.536
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg17.837
r_dihedral_angle_3_deg14.985
r_scangle_it6.415
r_dihedral_angle_1_deg6.11
r_scbond_it4.178
r_mcangle_it2.344
r_angle_refined_deg1.873
r_mcbond_it1.536
r_chiral_restr0.12
r_bond_refined_d0.015
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15640
Nucleic Acid Atoms
Solvent Atoms1343
Heterogen Atoms652

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing