3DSX

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DSSDB ENTRY 3DSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.228414% (w/v) PEG 3350, 0.2M Ca(OAc)2, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
2.3347.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.354α = 90
b = 91.153β = 90
c = 114.591γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9841SLSX10SA

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
12.13099.80.05723.47.24190941826539
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)
2.12.21000.3916.97.45348

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 REPLACEMENTTHROUGHOUTDB ENTRY 3DSS2.129.3739725210199.850.170560.167530.22942RANDOM30.065
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg18.592
r_dihedral_angle_3_deg16.294
r_dihedral_angle_1_deg5.676
r_scangle_it3.576
r_scbond_it2.397
r_mcangle_it1.867
r_angle_refined_deg1.285
r_mcbond_it1.166
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.612
r_dihedral_angle_4_deg18.592
r_dihedral_angle_3_deg16.294
r_dihedral_angle_1_deg5.676
r_scangle_it3.576
r_scbond_it2.397
r_mcangle_it1.867
r_angle_refined_deg1.285
r_mcbond_it1.166
r_angle_other_deg0.846
r_mcbond_other0.699
r_symmetry_hbond_refined0.263
r_symmetry_vdw_other0.262
r_nbd_refined0.215
r_nbtor_refined0.182
r_nbd_other0.18
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.156
r_metal_ion_refined0.099
r_nbtor_other0.087
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5089
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing