1Z22

GDP-Bound Rab23 GTPase crystallized in C222(1) space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPolyalanine Rab3a GTPase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627727% PEG 6000, 200mM Na Citrate, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.01α = 90
b = 71.333β = 90
c = 65.684γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic mirror2004-01-09MSINGLE 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
12.065099.90.09716.45100351005228.6
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)
2.062.1299.90.3064.35828

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 GTPase2.06610052912246399.940.2090.196060.194040.2343RANDOM20.757
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]
-0.7-0.841.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.462
r_dihedral_angle_3_deg14.31
r_dihedral_angle_4_deg13.402
r_dihedral_angle_1_deg5.921
r_scangle_it1.649
r_angle_refined_deg1.065
r_scbond_it1.019
r_mcangle_it0.815
r_mcbond_it0.47
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.462
r_dihedral_angle_3_deg14.31
r_dihedral_angle_4_deg13.402
r_dihedral_angle_1_deg5.921
r_scangle_it1.649
r_angle_refined_deg1.065
r_scbond_it1.019
r_mcangle_it0.815
r_mcbond_it0.47
r_nbtor_refined0.298
r_symmetry_vdw_refined0.191
r_nbd_refined0.189
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.126
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_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 Atoms1234
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing