1Z07

GppNHp-Bound Rab5c G55Q mutant GTPase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPolyalanine Rab5c GTPase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627710% PEG 6000, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1141.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.317α = 90
b = 64.008β = 90
c = 66.314γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateosmic mirror2004-01-02MSINGLE 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
11.85097.10.0581631269723.1
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)
1.81.8573.40.22953880

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 REPLACEMENTTHROUGHOUTPolyalanine Rab5c GTPase1.818145111193062486.650.1750.170370.167950.21904RANDOM15.35
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]
-0.370.44-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.941
r_dihedral_angle_3_deg10.599
r_dihedral_angle_1_deg5.036
r_dihedral_angle_4_deg4.364
r_angle_refined_deg1.065
r_nbtor_refined0.293
r_nbd_refined0.189
r_symmetry_vdw_refined0.137
r_xyhbond_nbd_refined0.106
r_symmetry_hbond_refined0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.941
r_dihedral_angle_3_deg10.599
r_dihedral_angle_1_deg5.036
r_dihedral_angle_4_deg4.364
r_angle_refined_deg1.065
r_nbtor_refined0.293
r_nbd_refined0.189
r_symmetry_vdw_refined0.137
r_xyhbond_nbd_refined0.106
r_symmetry_hbond_refined0.072
r_chiral_restr0.068
r_metal_ion_refined0.035
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1274
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing