3DCG

Crystal Structure of the HIV Vif BC-box in Complex with Human ElonginB and ElonginC


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72950.1M Tris HCl pH 7.0, 40% PEG 350 MME, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9938.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.514α = 90
b = 66.913β = 90
c = 122.642γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9794APS24-ID-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
12.429.3798.20.0960.09611.73.918219-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4997.30.4412.53.31762

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1vcb2.429.371724689598.120.188260.186030.23228RANDOM41.623
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]
-0.160.74-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.849
r_dihedral_angle_3_deg18.13
r_dihedral_angle_4_deg15.182
r_dihedral_angle_1_deg6.903
r_scangle_it4.485
r_scbond_it3.048
r_mcangle_it2.556
r_mcbond_it1.9
r_angle_refined_deg1.132
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.849
r_dihedral_angle_3_deg18.13
r_dihedral_angle_4_deg15.182
r_dihedral_angle_1_deg6.903
r_scangle_it4.485
r_scbond_it3.048
r_mcangle_it2.556
r_mcbond_it1.9
r_angle_refined_deg1.132
r_nbtor_refined0.306
r_symmetry_hbond_refined0.213
r_nbd_refined0.191
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.157
r_chiral_restr0.07
r_bond_refined_d0.008
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 Atoms3154
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing