1Z06

GppNHp-Bound Rab33 GTPase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% PEG 6000, 10% Glycerol, 1M Lithium Chlroride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7555

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.194α = 90
b = 56.194β = 90
c = 55.039γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateosmic mirror2003-02-25MSINGLE 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
11.85096.70.0572951743131.5
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)
1.81.8584.20.2497.751240

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 GTPase1.818174351635387997.520.2070.190820.189460.21794RANDOM22.211
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]
-0.43-0.21-0.430.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg15.906
r_dihedral_angle_3_deg12.23
r_dihedral_angle_1_deg5.458
r_scangle_it1.915
r_scbond_it1.349
r_angle_refined_deg1.275
r_mcangle_it1.059
r_mcbond_it0.965
r_angle_other_deg0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.74
r_dihedral_angle_4_deg15.906
r_dihedral_angle_3_deg12.23
r_dihedral_angle_1_deg5.458
r_scangle_it1.915
r_scbond_it1.349
r_angle_refined_deg1.275
r_mcangle_it1.059
r_mcbond_it0.965
r_angle_other_deg0.826
r_symmetry_vdw_other0.261
r_nbd_refined0.205
r_nbd_other0.182
r_nbtor_refined0.175
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.129
r_mcbond_other0.123
r_xyhbond_nbd_other0.096
r_symmetry_vdw_refined0.096
r_nbtor_other0.082
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
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 Atoms1269
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing