3WEH

Crystal structure of the human squalene synthase in complex with presqualene pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VJ8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529820% PEG 2000 MME, 0.01M NiCl2, 0.1M Tris, 1mM presqualene pyrophosphate, 1mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3547.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.235α = 90
b = 93.876β = 90
c = 108.803γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00000Photon FactoryAR-NW12A

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
11.873099.80.05730.55.83159731534132.1
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)
11.871.941000.5174.55.93095

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 REPLACEMENTTHROUGHOUT3VJ81.8728.7331342158399.150.167760.164970.21947RANDOM28.215
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]
3.33-2.14-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.829
r_dihedral_angle_4_deg14.513
r_dihedral_angle_3_deg14.51
r_scangle_it5.704
r_dihedral_angle_1_deg4.861
r_scbond_it3.631
r_mcangle_it2.342
r_rigid_bond_restr1.796
r_angle_refined_deg1.416
r_mcbond_it1.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.829
r_dihedral_angle_4_deg14.513
r_dihedral_angle_3_deg14.51
r_scangle_it5.704
r_dihedral_angle_1_deg4.861
r_scbond_it3.631
r_mcangle_it2.342
r_rigid_bond_restr1.796
r_angle_refined_deg1.416
r_mcbond_it1.355
r_chiral_restr0.099
r_bond_refined_d0.007
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2681
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms41

Software

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