1YZQ

GppNHp-Bound Rab6 GTPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727820% PEG 6000, 300mM Magnesium Chloride, 10% glycerol, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.7554.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.495α = 90
b = 68.672β = 90
c = 73.102γ = 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 mirror2003-05-13MSINGLE 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
11.785099.40.05827.762005936
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)
1.781.8395.10.2826.251576

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 Rab3a GTPase1.786201871849999299.510.2380.232370.23060.26488RANDOM27.115
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]
-1.43-0.421.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.778
r_dihedral_angle_4_deg21.833
r_dihedral_angle_3_deg14.088
r_dihedral_angle_1_deg4.987
r_scangle_it2.229
r_scbond_it1.552
r_angle_refined_deg1.177
r_mcangle_it0.953
r_mcbond_it0.607
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.778
r_dihedral_angle_4_deg21.833
r_dihedral_angle_3_deg14.088
r_dihedral_angle_1_deg4.987
r_scangle_it2.229
r_scbond_it1.552
r_angle_refined_deg1.177
r_mcangle_it0.953
r_mcbond_it0.607
r_nbtor_refined0.305
r_nbd_refined0.195
r_metal_ion_refined0.169
r_symmetry_hbond_refined0.15
r_symmetry_vdw_refined0.149
r_xyhbond_nbd_refined0.127
r_chiral_restr0.066
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 Atoms1288
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing