3E60

Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Bartonella henselae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17289ProPlex condition B12, 15% PEG 4000, 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 0.4/0.4uL drops, 6.5 mg/mL protein, Crystal ID 200083b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9157.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.339α = 90
b = 91.339β = 90
c = 251.177γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDSI(111) DOUBLE CRYSTAL MONOCHROMETER2008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
11.955099.90.12313.47.378307
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)
1.952.061000.5783.87.4

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 REPLACEMENTTHROUGHOUT1W0I WITH INSERTIONS REMOVED1.955078248385299.80.1660.1650.186RANDOM24.41
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]
0.380.38-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.357
r_dihedral_angle_3_deg13.512
r_dihedral_angle_4_deg13.469
r_dihedral_angle_1_deg5.245
r_scangle_it3.125
r_scbond_it1.82
r_angle_other_deg1.189
r_angle_refined_deg1.095
r_mcangle_it1.049
r_mcbond_it0.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.357
r_dihedral_angle_3_deg13.512
r_dihedral_angle_4_deg13.469
r_dihedral_angle_1_deg5.245
r_scangle_it3.125
r_scbond_it1.82
r_angle_other_deg1.189
r_angle_refined_deg1.095
r_mcangle_it1.049
r_mcbond_it0.526
r_mcbond_other0.106
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms6269
Nucleic Acid Atoms
Solvent Atoms779
Heterogen Atoms2

Software

Software
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling