4EA0

Crystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with diphosphate and quinuclidine BPH-651


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42980.75M POTASSIUM SODIUM TARTRATE, 1MM BPH-651 (LIGAND), 1MM DIPHOSPHATE, 2MM MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4549.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.324α = 90
b = 80.324β = 90
c = 180.822γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-10-28MSINGLE 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)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
12.125094.537084

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1232.463505835058185694.20.2250.2220.278RANDOM46.23
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]
1.330.661.33-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.846
r_dihedral_angle_3_deg20.758
r_dihedral_angle_4_deg20.645
r_dihedral_angle_1_deg6.934
r_scangle_it6.081
r_scbond_it4.083
r_mcangle_it2.593
r_mcbond_it1.468
r_angle_refined_deg0.692
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.846
r_dihedral_angle_3_deg20.758
r_dihedral_angle_4_deg20.645
r_dihedral_angle_1_deg6.934
r_scangle_it6.081
r_scbond_it4.083
r_mcangle_it2.593
r_mcbond_it1.468
r_angle_refined_deg0.692
r_chiral_restr0.06
r_gen_planes_refined0.016
r_bond_refined_d0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4784
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms76

Software

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