1YZK

GppNHp bound Rab11 GTPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277NaCl, Glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal Properties
Matthews coefficientSolvent content
2.754.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.946α = 90
b = 73.946β = 90
c = 148.197γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2003-06-05MSINGLE 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
125099.80.05831.671429334.1
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)
22.0699.80.2527.671139

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 Rab5c26142951299269799.810.1970.180060.177530.22829RANDOM22.315
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]
-0.3-0.30.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.01
r_dihedral_angle_4_deg13.849
r_dihedral_angle_3_deg11.381
r_dihedral_angle_1_deg5.213
r_scangle_it1.782
r_scbond_it1.196
r_angle_refined_deg1.067
r_angle_other_deg0.723
r_mcangle_it0.723
r_mcbond_it0.686
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.01
r_dihedral_angle_4_deg13.849
r_dihedral_angle_3_deg11.381
r_dihedral_angle_1_deg5.213
r_scangle_it1.782
r_scbond_it1.196
r_angle_refined_deg1.067
r_angle_other_deg0.723
r_mcangle_it0.723
r_mcbond_it0.686
r_symmetry_vdw_other0.294
r_nbd_refined0.2
r_symmetry_hbond_refined0.188
r_nbtor_refined0.174
r_nbd_other0.17
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.139
r_mcbond_other0.081
r_nbtor_other0.077
r_metal_ion_refined0.062
r_chiral_restr0.056
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms1309
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing