3DST

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate


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
2.3246.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.264α = 90
b = 90.618β = 90
c = 114.478γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0007SLSX10SA

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
11.929.499.40.04424.64.65587255563547
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)
1.9299.40.3085.44.57804

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 3DSS1.929.2152773279099.480.182160.180240.21953RANDOM37.192
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_deg34.853
r_dihedral_angle_4_deg19.517
r_dihedral_angle_3_deg16.229
r_dihedral_angle_1_deg10.728
r_scangle_it2.999
r_scbond_it2.064
r_mcangle_it1.497
r_angle_refined_deg1.375
r_mcbond_it0.936
r_angle_other_deg0.903
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_4_deg19.517
r_dihedral_angle_3_deg16.229
r_dihedral_angle_1_deg10.728
r_scangle_it2.999
r_scbond_it2.064
r_mcangle_it1.497
r_angle_refined_deg1.375
r_mcbond_it0.936
r_angle_other_deg0.903
r_metal_ion_refined0.506
r_mcbond_other0.346
r_symmetry_hbond_refined0.298
r_symmetry_vdw_other0.217
r_nbd_refined0.215
r_symmetry_vdw_refined0.199
r_nbd_other0.187
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.158
r_chiral_restr0.095
r_nbtor_other0.086
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5055
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing