2HXS

Crystal Structure of Rab28A GTPase in the Inactive (GDP-3'P-Bound) Form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YZKPDB ENTRY 1YZK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529320% PEG 3360, 100 mM NaCl, 100 mM Potassium Acetate, 5% glycerol, 20 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8433.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.51α = 90
b = 56.621β = 90
c = 85.109γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.13198.30.0750.07524.78.359785587821111.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.11.1496.80.3670.3674.255.15607

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YZK1.1315763955034294595.480.1520.1520.148670.1836RANDOM18.885
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]
0.980.06-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.25
r_dihedral_angle_4_deg15.846
r_dihedral_angle_3_deg12.531
r_sphericity_free11.829
r_sphericity_bonded6.65
r_scangle_it5.905
r_dihedral_angle_1_deg5.268
r_scbond_it4.531
r_mcangle_it3.513
r_rigid_bond_restr2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.25
r_dihedral_angle_4_deg15.846
r_dihedral_angle_3_deg12.531
r_sphericity_free11.829
r_sphericity_bonded6.65
r_scangle_it5.905
r_dihedral_angle_1_deg5.268
r_scbond_it4.531
r_mcangle_it3.513
r_rigid_bond_restr2.67
r_mcbond_it2.618
r_angle_refined_deg2.184
r_nbtor_refined0.322
r_symmetry_vdw_refined0.251
r_nbd_refined0.233
r_symmetry_hbond_refined0.196
r_xyhbond_nbd_refined0.142
r_chiral_restr0.139
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1503
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing