3CPJ

Crystal structure of Ypt31 in complex with yeast Rab-GDI


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UKVPDB ENTRY 1ukv, chain G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.94α = 90
b = 61.43β = 103.68
c = 92.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.931SLSX10SA

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
12.3519.7999.73077230683-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.352.499.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ukv, chain G2.3519.79287142871415121000.201560.201560.198750.25523RANDOM42.168
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.739
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg15.041
r_dihedral_angle_1_deg5.414
r_scangle_it1.791
r_angle_refined_deg1.102
r_scbond_it1.079
r_mcangle_it0.832
r_mcbond_it0.472
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.739
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg15.041
r_dihedral_angle_1_deg5.414
r_scangle_it1.791
r_angle_refined_deg1.102
r_scbond_it1.079
r_mcangle_it0.832
r_mcbond_it0.472
r_nbtor_refined0.298
r_nbd_refined0.19
r_symmetry_hbond_refined0.172
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.14
r_chiral_restr0.071
r_metal_ion_refined0.029
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4749
Nucleic Acid Atoms
Solvent Atoms452
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing