3T5G

Structure of fully modified farnesylated Rheb in complex with PDE6D


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XTQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22930.1 M Tris 8.5, and 12.5 % PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.89α = 90
b = 57.38β = 90
c = 134.52γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.979SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.73097.2404544045411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.895.70.285.956.76158

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1XTQ1.729.011384293842920231000.199440.199440.197570.23538RANDOM19.637
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]
-0.110.66-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.091
r_dihedral_angle_3_deg11.983
r_dihedral_angle_4_deg8.856
r_dihedral_angle_1_deg5.641
r_scangle_it2.699
r_scbond_it1.606
r_mcangle_it1.092
r_angle_refined_deg1.078
r_mcbond_it0.568
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.091
r_dihedral_angle_3_deg11.983
r_dihedral_angle_4_deg8.856
r_dihedral_angle_1_deg5.641
r_scangle_it2.699
r_scbond_it1.606
r_mcangle_it1.092
r_angle_refined_deg1.078
r_mcbond_it0.568
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2549
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms44

Software

Software
Software NamePurpose
ProDCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling