3PZ4

Crystal structure of FTase(ALPHA-subunit; BETA-subunit DELTA C10) in complex with BMS3 and lipid substrate FPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EU5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529220% (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1661.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.746α = 90
b = 170.746β = 90
c = 69.085γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.13099.80.06246.26724567104536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.21000.3596.56.18682

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 REPLACEMENTTHROUGHOUT3EU52.129.9163737336599.830.227330.225210.2674RANDOM36.501
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]
1.210.61.21-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.187
r_dihedral_angle_4_deg18.68
r_dihedral_angle_3_deg17.967
r_dihedral_angle_1_deg7.12
r_mcbond_other6.205
r_scangle_it4.725
r_angle_other_deg4.147
r_mcangle_it3.141
r_scbond_it2.806
r_mcbond_it1.839
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.187
r_dihedral_angle_4_deg18.68
r_dihedral_angle_3_deg17.967
r_dihedral_angle_1_deg7.12
r_mcbond_other6.205
r_scangle_it4.725
r_angle_other_deg4.147
r_mcangle_it3.141
r_scbond_it2.806
r_mcbond_it1.839
r_angle_refined_deg1.656
r_symmetry_hbond_refined0.465
r_symmetry_vdw_other0.305
r_symmetry_vdw_refined0.294
r_nbd_refined0.272
r_nbd_other0.256
r_xyhbond_nbd_refined0.236
r_nbtor_refined0.196
r_xyhbond_nbd_other0.12
r_chiral_restr0.113
r_nbtor_other0.11
r_bond_refined_d0.017
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5839
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms63

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling