4GTS

Engineered RabGGTase in complex with BMS analogue 16


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
2.3146.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.636α = 90
b = 91.366β = 90
c = 114.093γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2009-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.452098.30.07217.43.9262692581336.9
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)
12.452.5597.80.3784.13.9

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 REPLACEMENTTHROUGHOUT3DSS2.4519.992626924553125998.510.185820.182640.24771RANDOM36.071
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]
0.39-0.05-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.872
r_dihedral_angle_4_deg18.024
r_dihedral_angle_3_deg16.89
r_dihedral_angle_1_deg6.05
r_angle_other_deg4.214
r_scangle_it3.933
r_scbond_it2.778
r_mcangle_it1.742
r_angle_refined_deg1.544
r_mcbond_it1.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.872
r_dihedral_angle_4_deg18.024
r_dihedral_angle_3_deg16.89
r_dihedral_angle_1_deg6.05
r_angle_other_deg4.214
r_scangle_it3.933
r_scbond_it2.778
r_mcangle_it1.742
r_angle_refined_deg1.544
r_mcbond_it1.007
r_mcbond_other0.423
r_symmetry_vdw_other0.273
r_nbd_refined0.246
r_nbd_other0.239
r_xyhbond_nbd_refined0.204
r_nbtor_refined0.193
r_symmetry_vdw_refined0.135
r_metal_ion_refined0.134
r_nbtor_other0.107
r_chiral_restr0.089
r_symmetry_hbond_refined0.068
r_bond_refined_d0.015
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
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 Atoms4994
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms46

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling