3D04

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with sakuranetin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GLLPDB entry 2GLL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.82770.1M Sodium Acetate trihydrate, 2.0M Sodium Formate Additive, 20%(w/v) Benzamidine HCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1761.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.967α = 90
b = 100.312β = 90
c = 186.57γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.45099.80.1120.11212.85.855059
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)
2.42.531000.4090.4093.35.543850

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 2GLL2.419.9954994279399.780.1910.190.212RANDOM20.555
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]
0.49-1.220.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_3_deg14.839
r_dihedral_angle_4_deg9.305
r_dihedral_angle_1_deg5.487
r_scangle_it1.886
r_angle_refined_deg1.145
r_scbond_it1.129
r_mcangle_it0.815
r_mcbond_it0.483
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_3_deg14.839
r_dihedral_angle_4_deg9.305
r_dihedral_angle_1_deg5.487
r_scangle_it1.886
r_angle_refined_deg1.145
r_scbond_it1.129
r_mcangle_it0.815
r_mcbond_it0.483
r_nbtor_refined0.308
r_nbd_refined0.187
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.128
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7272
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms102

Software

Software
Software NamePurpose
MOSFLMdata reduction
d*TREKdata scaling
MOLREPphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction