8QUI | pdb_00008qui

Hexameric HIV-1 CA in complex with DDD00024969


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HGMHexameric HIV-1 CA in complex with dATP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52900.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Crystal Properties
Matthews coefficientSolvent content
2.7555.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.805α = 90
b = 91.805β = 90
c = 57.59γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2016-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.6928.899.80.0590.9920.49.231130
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.7398.60.620.782.66.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6928.829474156299.490.175290.173150.180.216180.22RANDOM28.33
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]
0.270.130.27-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.72
r_dihedral_angle_4_deg22.38
r_dihedral_angle_3_deg14.332
r_long_range_B_refined7.711
r_long_range_B_other7.526
r_dihedral_angle_1_deg6.02
r_scangle_other5.81
r_mcangle_other4.284
r_mcangle_it4.279
r_scbond_it3.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.72
r_dihedral_angle_4_deg22.38
r_dihedral_angle_3_deg14.332
r_long_range_B_refined7.711
r_long_range_B_other7.526
r_dihedral_angle_1_deg6.02
r_scangle_other5.81
r_mcangle_other4.284
r_mcangle_it4.279
r_scbond_it3.986
r_scbond_other3.984
r_angle_other_deg3.794
r_mcbond_it2.999
r_mcbond_other2.973
r_angle_refined_deg2.12
r_chiral_restr0.147
r_bond_refined_d0.027
r_gen_planes_other0.02
r_gen_planes_refined0.012
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1664
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing