2F7S

The crystal structure of human Rab27b bound to GDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529120%(v/v) isopropanol, 25%(v/v)PEG 4K, 0.1M sodium citrate, 0.1 M bistris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.469α = 90
b = 64.023β = 90
c = 153.32γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.978APS17-ID

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
12.695099.30.0537.66.6156581565811
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)
2.692.8296.10.215.695.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1OIV2.75011468780399.040.247650.245290.29248RANDOM57.722
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]
-0.726.17-5.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.488
r_dihedral_angle_3_deg20.28
r_dihedral_angle_4_deg19.123
r_dihedral_angle_1_deg6.359
r_angle_refined_deg1.486
r_nbtor_refined0.315
r_nbd_refined0.23
r_xyhbond_nbd_refined0.181
r_symmetry_vdw_refined0.174
r_metal_ion_refined0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.488
r_dihedral_angle_3_deg20.28
r_dihedral_angle_4_deg19.123
r_dihedral_angle_1_deg6.359
r_angle_refined_deg1.486
r_nbtor_refined0.315
r_nbd_refined0.23
r_xyhbond_nbd_refined0.181
r_symmetry_vdw_refined0.174
r_metal_ion_refined0.095
r_chiral_restr0.091
r_symmetry_hbond_refined0.043
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2887
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing