3ZU4 | pdb_00003zu4

Structure of the enoyl-ACP reductase FabV from Yersinia pestis with the cofactor NADH and the 2-pyridone inhibitor PT172


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
135% PEG 4000, 150 MM AMMONIUM SULFATE, 100 MM MES PH 5.5.
Crystal Properties
Matthews coefficientSolvent content
2.8256

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.84α = 90
b = 101.84β = 90
c = 84.75γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
1244.11000.0714.24.4342933

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0188.232533173399.980.178090.17590.190.220580.23RANDOM39.589
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]
1.250.621.25-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.396
r_dihedral_angle_4_deg24.247
r_dihedral_angle_3_deg14.284
r_dihedral_angle_1_deg5.896
r_scangle_it3.815
r_scbond_it2.319
r_angle_refined_deg1.471
r_mcangle_it1.42
r_mcbond_it0.758
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.396
r_dihedral_angle_4_deg24.247
r_dihedral_angle_3_deg14.284
r_dihedral_angle_1_deg5.896
r_scangle_it3.815
r_scbond_it2.319
r_angle_refined_deg1.471
r_mcangle_it1.42
r_mcbond_it0.758
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms3091
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing