8QUL

Hexameric HIV-1 CA in complex with DDD00100555


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
2.6453.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.65α = 90
b = 90.65β = 90
c = 56.68γ = 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)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
11.6756.681000.0719.41030894
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)
11.671.71001.41.89.2

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6756.682935615381000.1770.1750.21RANDOM31.18
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]
-0.07-0.04-0.070.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.277
r_dihedral_angle_4_deg22.722
r_dihedral_angle_3_deg14.223
r_long_range_B_refined7.658
r_long_range_B_other7.542
r_scangle_other6.229
r_dihedral_angle_1_deg6.065
r_mcangle_it4.361
r_mcangle_other4.361
r_scbond_it4.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.277
r_dihedral_angle_4_deg22.722
r_dihedral_angle_3_deg14.223
r_long_range_B_refined7.658
r_long_range_B_other7.542
r_scangle_other6.229
r_dihedral_angle_1_deg6.065
r_mcangle_it4.361
r_mcangle_other4.361
r_scbond_it4.349
r_scbond_other4.347
r_angle_other_deg3.696
r_mcbond_it3.224
r_mcbond_other3.222
r_angle_refined_deg2.278
r_chiral_restr0.146
r_bond_refined_d0.027
r_gen_planes_other0.021
r_gen_planes_refined0.013
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 Atoms1670
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing