3DSV

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.228414% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
2.3146.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.035α = 90
b = 90.613β = 90
c = 114.376γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

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
12.13099.90.0853118.54139541339530
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)
2.12.299.70.37911.116.55293

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 3DSS2.129.239268207199.920.152310.149270.21114RANDOM25.886
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]
1.73-0.44-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.766
r_dihedral_angle_4_deg19.937
r_dihedral_angle_3_deg16.373
r_dihedral_angle_1_deg12.981
r_angle_other_deg3.745
r_scangle_it3.701
r_scbond_it2.394
r_mcangle_it1.968
r_angle_refined_deg1.456
r_mcbond_it1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.766
r_dihedral_angle_4_deg19.937
r_dihedral_angle_3_deg16.373
r_dihedral_angle_1_deg12.981
r_angle_other_deg3.745
r_scangle_it3.701
r_scbond_it2.394
r_mcangle_it1.968
r_angle_refined_deg1.456
r_mcbond_it1.1
r_mcbond_other1.034
r_symmetry_hbond_refined0.443
r_nbd_other0.234
r_symmetry_vdw_other0.228
r_nbd_refined0.22
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.182
r_nbtor_other0.107
r_chiral_restr0.104
r_xyhbond_nbd_other0.074
r_metal_ion_refined0.059
r_symmetry_metal_ion_refined0.017
r_bond_refined_d0.011
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d
r_metal_ion_other
r_symmetry_hbond_other
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 Atoms5093
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing