1Z0K

Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherRab4 GTPase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629120% PEG 4000, 200mM ammonium fluoride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5851.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.44α = 90
b = 81.44β = 90
c = 137.639γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateosmic mirror2004-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.95099.60.05427.2954219341.7
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)
1.91.9698.90.379453439

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 REPLACEMENTTHROUGHOUTRab4 GTPase1.92154221438744207299.680.240.225380.223560.25889RANDOM33.045
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]
1.20.61.2-1.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.918
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg12.886
r_dihedral_angle_1_deg5.341
r_scangle_it1.953
r_angle_refined_deg1.302
r_scbond_it1.243
r_mcangle_it1.053
r_mcbond_it0.626
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.918
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg12.886
r_dihedral_angle_1_deg5.341
r_scangle_it1.953
r_angle_refined_deg1.302
r_scbond_it1.243
r_mcangle_it1.053
r_mcbond_it0.626
r_nbtor_refined0.297
r_nbd_refined0.192
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.143
r_metal_ion_refined0.126
r_chiral_restr0.114
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3573
Nucleic Acid Atoms
Solvent Atoms457
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing