3Q30

Human Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-3-[5-(2-naphthalenyl)pentyl]aminocarbonyl-3-[5-(2-naphthalenyl)pentyloxy]propionic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EZFPDB ENTRY 1EZF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5293seeding method, pH 5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.973α = 90
b = 59.526β = 115.71
c = 84.139γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IICmonochromator2000-03-19MSINGLE 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
1225990.065102.592577125771
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)
122.0799.80.31132.532567

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1EZF225257632452812351000.208330.208330.206860.2375RANDOM29.838
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]
0.22-1.81-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.716
r_dihedral_angle_4_deg16.026
r_dihedral_angle_3_deg14.782
r_dihedral_angle_1_deg5.324
r_scangle_it2.379
r_mcangle_it1.627
r_scbond_it1.581
r_angle_refined_deg1.469
r_mcbond_it0.953
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.716
r_dihedral_angle_4_deg16.026
r_dihedral_angle_3_deg14.782
r_dihedral_angle_1_deg5.324
r_scangle_it2.379
r_mcangle_it1.627
r_scbond_it1.581
r_angle_refined_deg1.469
r_mcbond_it0.953
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms2628
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms51

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling