1Z0D

GDP-Bound Rab5c GTPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529110% PEG 4000, 200mM Lithium Sulfate, 50mM Na acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6152.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.401α = 90
b = 70.931β = 90
c = 137.61γ = 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 mirror2004-08-04MSINGLE 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
12.25098.60.0881751964137.5
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)
2.22.2697.50.407451609

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 GTPase2.28196411812398398.540.2010.189130.186090.24685RANDOM28.211
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]
-0.661.28-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.358
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.077
r_dihedral_angle_1_deg5.37
r_scangle_it1.758
r_angle_refined_deg1.112
r_scbond_it1.046
r_mcangle_it0.825
r_mcbond_it0.459
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.358
r_dihedral_angle_3_deg12.87
r_dihedral_angle_4_deg12.077
r_dihedral_angle_1_deg5.37
r_scangle_it1.758
r_angle_refined_deg1.112
r_scbond_it1.046
r_mcangle_it0.825
r_mcbond_it0.459
r_nbtor_refined0.297
r_nbd_refined0.189
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.111
r_chiral_restr0.069
r_bond_refined_d0.007
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_refined
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 Atoms2504
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing