8QUK | pdb_00008quk

Hexameric HIV-1 CA in complex with DDD00100439


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
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.61α = 90
b = 90.61β = 90
c = 56.8γ = 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
11.3845.3194.40.040.99247.951571
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)
11.381.463.20.640.581.62.4

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 REPLACEMENTTHROUGHOUT1.3845.3149028254194.350.177960.176590.180.202990.21RANDOM29.869
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]
0.30.150.3-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg26.807
r_long_range_B_other14.771
r_long_range_B_refined14.713
r_dihedral_angle_3_deg14.009
r_mcangle_other12.293
r_mcangle_it12.292
r_mcbond_it11.728
r_mcbond_other11.725
r_scangle_other10.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg26.807
r_long_range_B_other14.771
r_long_range_B_refined14.713
r_dihedral_angle_3_deg14.009
r_mcangle_other12.293
r_mcangle_it12.292
r_mcbond_it11.728
r_mcbond_other11.725
r_scangle_other10.847
r_scbond_it8.09
r_scbond_other8.086
r_dihedral_angle_1_deg5.968
r_angle_other_deg3.711
r_angle_refined_deg2.178
r_chiral_restr0.138
r_bond_refined_d0.028
r_gen_planes_other0.022
r_gen_planes_refined0.011
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 Atoms1696
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing