3ADZ

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529811-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris, 0.5 mM PSPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4649.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.685α = 90
b = 80.685β = 90
c = 90.794γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Vertically Collimating Premirror, Toroidal Focusing Mirror2009-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0000NSRRCBL13B1

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
11.893099.90.03149.47.327854278211
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)
11.891.961000.3235.27.52720

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 REPLACEMENTTHROUGHOUT2ZCO1.893026389139599.860.170710.16820.22236RANDOM24.272
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]
1.050.521.05-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.562
r_dihedral_angle_4_deg19.908
r_dihedral_angle_3_deg14.682
r_sphericity_free6.974
r_dihedral_angle_1_deg5.114
r_scangle_it4.964
r_sphericity_bonded3.652
r_scbond_it3.324
r_rigid_bond_restr2.225
r_mcangle_it2.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.562
r_dihedral_angle_4_deg19.908
r_dihedral_angle_3_deg14.682
r_sphericity_free6.974
r_dihedral_angle_1_deg5.114
r_scangle_it4.964
r_sphericity_bonded3.652
r_scbond_it3.324
r_rigid_bond_restr2.225
r_mcangle_it2.198
r_mcbond_it1.383
r_angle_refined_deg1.329
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms2385
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms41

Software

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