X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPolyalanine Rab4 GTPase

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP627720% PEG 6000, 200mM Magnesium Chloride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal Properties
Matthews coefficientSolvent content
2.8656.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.325α = 90
b = 68.325β = 90
c = 83.229γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateosmic mirror2003-08-21MSINGLE 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
11.855099.20.0626.271940932.8
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)
1.851.90.3945719418

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 Rab4 GTPase1.854.8194181730892599.620.2150.193270.191790.22084RANDOM21.02
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.622
r_dihedral_angle_4_deg20.894
r_dihedral_angle_3_deg11.797
r_dihedral_angle_1_deg5.804
r_scangle_it1.914
r_scbond_it1.344
r_angle_refined_deg1.158
r_mcangle_it0.958
r_mcbond_it0.884
r_angle_other_deg0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.622
r_dihedral_angle_4_deg20.894
r_dihedral_angle_3_deg11.797
r_dihedral_angle_1_deg5.804
r_scangle_it1.914
r_scbond_it1.344
r_angle_refined_deg1.158
r_mcangle_it0.958
r_mcbond_it0.884
r_angle_other_deg0.81
r_nbd_refined0.214
r_nbd_other0.185
r_symmetry_hbond_refined0.185
r_nbtor_refined0.182
r_symmetry_vdw_other0.16
r_xyhbond_nbd_refined0.154
r_xyhbond_nbd_other0.119
r_symmetry_vdw_refined0.104
r_mcbond_other0.103
r_nbtor_other0.079
r_chiral_restr0.067
r_metal_ion_refined0.027
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms1369
Nucleic Acid Atoms
Solvent Atoms253
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing