3DSW

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys(GG)-Ser-Cys 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
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.051α = 90
b = 90.908β = 90
c = 114.343γ = 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 X10SA0.9825SLSX10SA

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
12.1529.499.10.07215.243874638414539
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)
2.152.2599.80.3735.24.14857

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 3DSS2.1529.2136498191699.20.172780.16980.23154RANDOM36.193
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]
0.371.09-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.281
r_dihedral_angle_4_deg19.081
r_dihedral_angle_3_deg17.231
r_dihedral_angle_1_deg11.459
r_scangle_it4.269
r_angle_other_deg3.733
r_mcbond_other3.221
r_scbond_it2.759
r_mcangle_it2.44
r_angle_refined_deg1.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.281
r_dihedral_angle_4_deg19.081
r_dihedral_angle_3_deg17.231
r_dihedral_angle_1_deg11.459
r_scangle_it4.269
r_angle_other_deg3.733
r_mcbond_other3.221
r_scbond_it2.759
r_mcangle_it2.44
r_angle_refined_deg1.446
r_mcbond_it1.391
r_symmetry_hbond_refined0.416
r_nbd_other0.23
r_nbd_refined0.22
r_symmetry_vdw_other0.214
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.179
r_metal_ion_refined0.162
r_chiral_restr0.136
r_symmetry_vdw_refined0.126
r_nbtor_other0.107
r_bond_refined_d0.012
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_bond_other_d
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 Atoms5095
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing