3PZ2

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP


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
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.448α = 90
b = 84.582β = 90
c = 117.973γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

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
12.353099.40.06317.54.92837528201542.4
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)
12.352.45990.3777.153230

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 REPLACEMENTTHROUGHOUT3DSS2.353026810140399.50.190950.187610.25551RANDOM37.329
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]
-1.181.47-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg19.375
r_dihedral_angle_4_deg18.32
r_dihedral_angle_1_deg7.416
r_scangle_it5.164
r_angle_other_deg4.262
r_mcbond_other4.144
r_scbond_it3.523
r_mcangle_it2.638
r_angle_refined_deg1.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_3_deg19.375
r_dihedral_angle_4_deg18.32
r_dihedral_angle_1_deg7.416
r_scangle_it5.164
r_angle_other_deg4.262
r_mcbond_other4.144
r_scbond_it3.523
r_mcangle_it2.638
r_angle_refined_deg1.622
r_mcbond_it1.567
r_symmetry_vdw_other0.288
r_symmetry_hbond_refined0.269
r_nbd_other0.256
r_nbd_refined0.243
r_xyhbond_nbd_refined0.22
r_symmetry_vdw_refined0.218
r_nbtor_refined0.188
r_symmetry_metal_ion_refined0.183
r_nbtor_other0.114
r_chiral_restr0.096
r_metal_ion_refined0.047
r_bond_refined_d0.018
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4920
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms69

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling