3VJE

Crystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus in complex with zaragozic acid A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529811-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris pH 8.5, 0.25mM zaragozic acid A, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.177α = 90
b = 80.177β = 90
c = 185.414γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEHORIZONTAL FOCUSING MIRROR2010-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
12.123099.50.07133.694004739844150.3
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)
12.122.299.90.4854.893912

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ZCO2.1228.339655199299.220.207640.205090.25401RANDOM48.162
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]
0.690.340.69-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.845
r_dihedral_angle_3_deg16.7
r_dihedral_angle_4_deg16.666
r_dihedral_angle_1_deg5.472
r_scangle_it4.528
r_scbond_it2.835
r_mcangle_it2.053
r_rigid_bond_restr1.424
r_angle_refined_deg1.396
r_mcbond_it1.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.845
r_dihedral_angle_3_deg16.7
r_dihedral_angle_4_deg16.666
r_dihedral_angle_1_deg5.472
r_scangle_it4.528
r_scbond_it2.835
r_mcangle_it2.053
r_rigid_bond_restr1.424
r_angle_refined_deg1.396
r_mcbond_it1.131
r_chiral_restr0.103
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4770
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms98

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling