3GNS

Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (one molecule in AU)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PD3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529510~15% PEG 400, 0.1M Tris pH 8.3~8.5, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5852.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.877α = 90
b = 74.716β = 90
c = 110.652γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702008-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C11.000PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.750980.080.28198763472612243
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8560.130.282.953.4451

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2PD32.70637.667261726134791.810.214760.210990.28857RANDOM42.514
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]
-0.3-0.50.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg31.784
r_dihedral_angle_3_deg26.358
r_dihedral_angle_1_deg14.036
r_scangle_it7.319
r_scbond_it4.598
r_angle_refined_deg3.86
r_mcangle_it3.239
r_mcbond_it1.765
r_symmetry_hbond_refined0.979
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.95
r_dihedral_angle_4_deg31.784
r_dihedral_angle_3_deg26.358
r_dihedral_angle_1_deg14.036
r_scangle_it7.319
r_scbond_it4.598
r_angle_refined_deg3.86
r_mcangle_it3.239
r_mcbond_it1.765
r_symmetry_hbond_refined0.979
r_symmetry_vdw_refined0.447
r_nbtor_refined0.37
r_nbd_refined0.366
r_chiral_restr0.309
r_xyhbond_nbd_refined0.282
r_metal_ion_refined0.189
r_bond_refined_d0.048
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1704
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms1

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling