3V66

HUMAN SQUALENE SYNTHASE IN COMPLEX WITH 2-(1-{2-[(4R,6S)-8-chloro-6-(2,3-dimethoxyphenyl)-4H,6H-pyrrolo[1,2-a][4,1]benzoxazepin-4-yl]acetyl}-4-piperidinyl)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q30PDB ENTRY 3Q30

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5293CO-CRYSTALLIZED USING SEEDING METHOD., pH 5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.438α = 90
b = 60.144β = 117.14
c = 85.797γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICmirrors2004-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.810095.40.0747.72.423519635196
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)
11.81.8691.10.1732.323377

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 3Q301.8253340117711000.198720.197390.22383RANDOM21.879
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]
0.65-0.55-0.76-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg4.515
r_scangle_it2.28
r_mcangle_it1.569
r_scbond_it1.512
r_angle_refined_deg1.345
r_mcbond_it1.05
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg4.515
r_scangle_it2.28
r_mcangle_it1.569
r_scbond_it1.512
r_angle_refined_deg1.345
r_mcbond_it1.05
r_nbtor_refined0.31
r_symmetry_vdw_refined0.231
r_symmetry_hbond_refined0.217
r_nbd_refined0.207
r_xyhbond_nbd_refined0.152
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2662
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling