3OP4

Crystal structure of putative 3-ketoacyl-(acyl-carrier-protein) reductase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with NADP+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92932M NH4 Sulfate,0.1M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.058α = 90
b = 104.095β = 90
c = 126.07γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirror2010-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

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
11.6501000.10.128.96.56143361433-315.4
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)
11.61.631000.6160.6163.36.53009

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.6505828158281310699.620.148720.148720.147330.1751RANDOM17.407
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]
0.360.13-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.637
r_dihedral_angle_4_deg19.783
r_dihedral_angle_3_deg12.808
r_dihedral_angle_1_deg5.825
r_scangle_it5.397
r_scbond_it3.655
r_mcangle_it1.868
r_angle_refined_deg1.818
r_mcbond_it1.075
r_angle_other_deg1.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.637
r_dihedral_angle_4_deg19.783
r_dihedral_angle_3_deg12.808
r_dihedral_angle_1_deg5.825
r_scangle_it5.397
r_scbond_it3.655
r_mcangle_it1.868
r_angle_refined_deg1.818
r_mcbond_it1.075
r_angle_other_deg1.015
r_mcbond_other0.335
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3615
Nucleic Acid Atoms
Solvent Atoms503
Heterogen Atoms104

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing