4E9Z

Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with quinuclidine BPH-651 in the S1 site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.40.2M POTASSIUM SODIUM TARTRATE, 20% W/ V PEG 3350, 1MM PPI, 1MM BPH-651 (LIGAND), pH 7.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.550.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.589α = 90
b = 80.589β = 90
c = 91.759γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-FAPS21-ID-F

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
12.065099.90.07312.7216152159422

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZCO2.063022074620373109398.20.1930.1910.241RANDOM34
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]
0.370.180.37-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_4_deg17.626
r_dihedral_angle_3_deg15.753
r_scangle_it6.227
r_dihedral_angle_1_deg5.794
r_scbond_it3.948
r_mcangle_it2.435
r_angle_refined_deg1.331
r_mcbond_it1.315
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_4_deg17.626
r_dihedral_angle_3_deg15.753
r_scangle_it6.227
r_dihedral_angle_1_deg5.794
r_scbond_it3.948
r_mcangle_it2.435
r_angle_refined_deg1.331
r_mcbond_it1.315
r_chiral_restr0.115
r_bond_refined_d0.015
r_gen_planes_refined0.012
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2392
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms21

Software

Software
Software NamePurpose
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling