3PZ1

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3


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
2.346.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.554α = 90
b = 90.583β = 90
c = 114.61γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9764SLSX10SA

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
11.9530990.04819.74.15123950703531.8
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)
11.952.0598.60.3315.54.26920

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 REPLACEMENTTHROUGHOUT3DSS1.9529.448147254298.970.184690.182270.23191RANDOM29.089
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]
-0.070.16-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.35
r_dihedral_angle_4_deg16.112
r_dihedral_angle_3_deg14.688
r_dihedral_angle_1_deg5.474
r_angle_other_deg4.158
r_scangle_it3.455
r_mcbond_other2.735
r_scbond_it2.296
r_mcangle_it1.811
r_angle_refined_deg1.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.35
r_dihedral_angle_4_deg16.112
r_dihedral_angle_3_deg14.688
r_dihedral_angle_1_deg5.474
r_angle_other_deg4.158
r_scangle_it3.455
r_mcbond_other2.735
r_scbond_it2.296
r_mcangle_it1.811
r_angle_refined_deg1.171
r_mcbond_it1.063
r_symmetry_vdw_other0.354
r_symmetry_vdw_refined0.243
r_nbd_other0.229
r_nbd_refined0.214
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.163
r_metal_ion_refined0.126
r_nbtor_other0.106
r_chiral_restr0.075
r_symmetry_metal_ion_refined0.049
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 Atoms4991
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms56

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling