3III

1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SACOL2612) from Staphylococcus aureus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293suberic acid, sebacic acid, hexadecanedioic acid, dodecanedioic acid 12mM each, PEG3350 20%, Hepes 0.1M pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.498α = 90
b = 74.498β = 90
c = 210.681γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793APS19-BM

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
11.9542.141000.1120.11229.116.24445244452-3
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)
11.951.981000.6370.6374.115.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9542.144201042010223299.910.146690.144740.18336RANDOM8.694
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]
0.160.16-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.283
r_dihedral_angle_4_deg17.327
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg6.854
r_scangle_it3.978
r_scbond_it2.77
r_angle_other_deg2.217
r_angle_refined_deg1.605
r_mcangle_it1.466
r_mcbond_it0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.283
r_dihedral_angle_4_deg17.327
r_dihedral_angle_3_deg12.63
r_dihedral_angle_1_deg6.854
r_scangle_it3.978
r_scbond_it2.77
r_angle_other_deg2.217
r_angle_refined_deg1.605
r_mcangle_it1.466
r_mcbond_it0.899
r_mcbond_other0.15
r_chiral_restr0.107
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_gen_planes_other0.006
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 Atoms4506
Nucleic Acid Atoms
Solvent Atoms556
Heterogen Atoms15

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP4model building
Omodel building
Cootmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
CCP4phasing