3PZ3

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.228414% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K
Crystal Properties
Matthews coefficientSolvent content
2.3247.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.732α = 90
b = 91.332β = 90
c = 114.652γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9770SLSX10SA

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
1220990.04120.53.74807747598537.3
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)
122.199.60.3544.83.76416

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 REPLACEMENTTHROUGHOUT3DSS22045177238999.070.180720.178490.22368RANDOM36.218
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]
1.15-0.28-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg18.751
r_dihedral_angle_3_deg15.386
r_dihedral_angle_1_deg5.075
r_scangle_it4.278
r_angle_other_deg4.179
r_mcbond_other3.066
r_scbond_it2.697
r_mcangle_it2.078
r_mcbond_it1.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg18.751
r_dihedral_angle_3_deg15.386
r_dihedral_angle_1_deg5.075
r_scangle_it4.278
r_angle_other_deg4.179
r_mcbond_other3.066
r_scbond_it2.697
r_mcangle_it2.078
r_mcbond_it1.207
r_angle_refined_deg1.194
r_xyhbond_nbd_other0.364
r_symmetry_vdw_other0.306
r_nbd_other0.231
r_nbd_refined0.214
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.182
r_metal_ion_refined0.165
r_symmetry_hbond_refined0.151
r_nbtor_other0.109
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_other0.006
r_gen_planes_refined0.004
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5006
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms56

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling