3DPU

RocCOR domain tandem of Rab family protein (Roco)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES (pH7.0), 1M Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4950.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 106.1β = 90
c = 139γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97892SLSX10SA

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
12.950990.0710.0620.523.72774027475-351.197
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)
12.9399.70.4660.3984.23.72635

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 3DPT2.947.67-32610113741000.232260.230290.27005RANDOM48.099
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]
2.68-0.76-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.169
r_dihedral_angle_3_deg19.807
r_dihedral_angle_4_deg18.064
r_dihedral_angle_1_deg5.959
r_scangle_it1.611
r_angle_refined_deg1.3
r_scbond_it0.951
r_mcangle_it0.676
r_mcbond_it0.374
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.169
r_dihedral_angle_3_deg19.807
r_dihedral_angle_4_deg18.064
r_dihedral_angle_1_deg5.959
r_scangle_it1.611
r_angle_refined_deg1.3
r_scbond_it0.951
r_mcangle_it0.676
r_mcbond_it0.374
r_nbtor_refined0.313
r_nbd_refined0.22
r_symmetry_hbond_refined0.185
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.151
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6235
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing