X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827718% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7554.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.357α = 90
b = 36.567β = 113.4
c = 86.666γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic mirror2004-04-14MSINGLE 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
12.055099.80.0815.842394635.1
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)
2.052.1198.10.3683.841952

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 GTPase2.05122411622613121999.880.2320.214250.210410.28586RANDOM23.139
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]
-0.84-0.90.66-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg19.942
r_dihedral_angle_3_deg13.691
r_dihedral_angle_1_deg6.137
r_scangle_it2.43
r_scbond_it1.8
r_angle_refined_deg1.26
r_mcbond_it1.105
r_mcangle_it1.028
r_angle_other_deg0.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.772
r_dihedral_angle_4_deg19.942
r_dihedral_angle_3_deg13.691
r_dihedral_angle_1_deg6.137
r_scangle_it2.43
r_scbond_it1.8
r_angle_refined_deg1.26
r_mcbond_it1.105
r_mcangle_it1.028
r_angle_other_deg0.755
r_xyhbond_nbd_refined0.211
r_nbd_refined0.209
r_symmetry_hbond_refined0.2
r_nbd_other0.196
r_symmetry_vdw_other0.18
r_nbtor_refined0.175
r_symmetry_vdw_refined0.154
r_mcbond_other0.105
r_nbtor_other0.082
r_chiral_restr0.069
r_xyhbond_nbd_other0.042
r_metal_ion_refined0.042
r_bond_refined_d0.01
r_bond_other_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.001
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 Atoms2395
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing