3AE0

Crystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with geranylgeranyl thiopyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZCP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529811-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris, 0.5mM GGsPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4549.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.118α = 90
b = 80.118β = 90
c = 183.617γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
12.373099.10.05632.56.228590283351
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)
12.372.4597.50.5813.15.72767

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 REPLACEMENTTHROUGHOUT2ZCP2.373026857142898.980.222340.219250.28055RANDOM31.492
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]
1.640.821.64-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.015
r_dihedral_angle_3_deg19.007
r_dihedral_angle_4_deg14.831
r_sphericity_free9.735
r_dihedral_angle_1_deg5.544
r_scangle_it4.715
r_sphericity_bonded3.154
r_scbond_it3.108
r_mcangle_it2.18
r_rigid_bond_restr2.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.015
r_dihedral_angle_3_deg19.007
r_dihedral_angle_4_deg14.831
r_sphericity_free9.735
r_dihedral_angle_1_deg5.544
r_scangle_it4.715
r_sphericity_bonded3.154
r_scbond_it3.108
r_mcangle_it2.18
r_rigid_bond_restr2.122
r_angle_refined_deg1.522
r_mcbond_it1.262
r_chiral_restr0.105
r_bond_refined_d0.007
r_gen_planes_refined0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4772
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms122

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing