4D45

Crystal structure of S. aureus FabI in complex with NADP and 5-bromo- 2-(4-chloro-2-hydroxyphenoxy)benzonitrile


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, 47% MPD
Crystal Properties
Matthews coefficientSolvent content
2.9658.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.077α = 98.43
b = 95.168β = 97.53
c = 95.2γ = 111.47
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-04-10MSINGLE 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
12.1546.5898.20.18.33.61522276
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)
12.152.2797.60.562.23.7

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 4ALK2.1546.58144551767698.180.176840.174170.22679RANDOM36.78
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]
3.60.16-0.27-1.68-1.55-2.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.071
r_dihedral_angle_3_deg16.296
r_dihedral_angle_4_deg15.73
r_dihedral_angle_1_deg6.867
r_scangle_it5.468
r_scbond_it3.794
r_mcangle_it2.074
r_angle_refined_deg1.682
r_mcbond_it1.323
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.071
r_dihedral_angle_3_deg16.296
r_dihedral_angle_4_deg15.73
r_dihedral_angle_1_deg6.867
r_scangle_it5.468
r_scbond_it3.794
r_mcangle_it2.074
r_angle_refined_deg1.682
r_mcbond_it1.323
r_chiral_restr0.091
r_gen_planes_refined0.013
r_bond_refined_d0.012
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 Atoms1016
Heterogen Atoms588

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing