X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527715% PEG 4000, 10% Glycerol, 200mM Na thiocyanate, 50mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8756.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.834α = 90
b = 99.719β = 90
c = 105.76γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateOsmic mirror2003-09-16MSINGLE 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
12.55095.60.06721.251385255.7
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)
2.52.5799.20.3874.851169

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 GTPase2.516138571312167995.40.250.217440.213540.29285RANDOM41.242
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]
-3.366.5-3.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.517
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg15.936
r_dihedral_angle_1_deg6.42
r_scangle_it1.908
r_angle_refined_deg1.42
r_scbond_it1.321
r_mcangle_it1.004
r_mcbond_it0.823
r_angle_other_deg0.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.517
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg15.936
r_dihedral_angle_1_deg6.42
r_scangle_it1.908
r_angle_refined_deg1.42
r_scbond_it1.321
r_mcangle_it1.004
r_mcbond_it0.823
r_angle_other_deg0.811
r_symmetry_hbond_refined0.259
r_nbd_refined0.245
r_symmetry_vdw_other0.241
r_symmetry_vdw_refined0.23
r_xyhbond_nbd_refined0.204
r_nbd_other0.195
r_nbtor_refined0.183
r_metal_ion_refined0.155
r_mcbond_other0.105
r_nbtor_other0.084
r_chiral_restr0.076
r_xyhbond_nbd_other0.013
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms2490
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing