4GTV

Engineered RabGGTase in complex with BMS analogue 13


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2285RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.3347.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.625α = 90
b = 90.741β = 90
c = 115.539γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9879SLSX10SA

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
11.9519.9998.70.06216.94.9518135113432.1
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)
11.95298.40.3615.24.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DSS1.9519.995181348526256598.730.170450.168350.21143RANDOM27.672
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]
0.92-0.64-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg19.991
r_dihedral_angle_3_deg14.879
r_dihedral_angle_1_deg5.341
r_angle_other_deg4.188
r_scangle_it3.581
r_scbond_it2.291
r_mcbond_other2.193
r_mcangle_it1.791
r_angle_refined_deg1.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg19.991
r_dihedral_angle_3_deg14.879
r_dihedral_angle_1_deg5.341
r_angle_other_deg4.188
r_scangle_it3.581
r_scbond_it2.291
r_mcbond_other2.193
r_mcangle_it1.791
r_angle_refined_deg1.121
r_mcbond_it1.024
r_symmetry_vdw_other0.27
r_nbd_other0.233
r_nbd_refined0.219
r_xyhbond_nbd_refined0.212
r_xyhbond_nbd_other0.202
r_symmetry_vdw_refined0.2
r_symmetry_hbond_refined0.186
r_nbtor_refined0.177
r_nbtor_other0.106
r_chiral_restr0.072
r_metal_ion_refined0.071
r_symmetry_metal_ion_refined0.059
r_bond_refined_d0.009
r_gen_planes_other0.005
r_gen_planes_refined0.004
r_bond_other_d
r_metal_ion_other
r_symmetry_hbond_other
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 Atoms4986
Nucleic Acid Atoms
Solvent Atoms379
Heterogen Atoms48

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling