3WEI

Crystal structure of the human squalene synthase Y73A mutant 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 DROP7.529820% PEG 4000, 10% 2-propanol, 0.1M HEPES, 1mM presqualene pyrophosphate, 3mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.193α = 90
b = 106.306β = 90
c = 33.108γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEHORIZONTAL FOCUSING MIRROR2011-04-16MSINGLE 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
11.793099.90.07130.473225632235127.2
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)
11.791.851000.5034.47.13164

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 REPLACEMENTTHROUGHOUT3VJ81.793032076162699.570.152750.149830.20883RANDOM25.748
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]
-1.7-1.643.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.387
r_dihedral_angle_4_deg19.23
r_dihedral_angle_3_deg13.824
r_scangle_it5.253
r_dihedral_angle_1_deg4.734
r_scbond_it3.374
r_mcangle_it2.142
r_rigid_bond_restr1.7
r_angle_refined_deg1.397
r_mcbond_it1.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.387
r_dihedral_angle_4_deg19.23
r_dihedral_angle_3_deg13.824
r_scangle_it5.253
r_dihedral_angle_1_deg4.734
r_scbond_it3.374
r_mcangle_it2.142
r_rigid_bond_restr1.7
r_angle_refined_deg1.397
r_mcbond_it1.236
r_chiral_restr0.094
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 Atoms2692
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms42

Software

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