8QUH

Hexameric HIV-1 CA in complex with DDD00057456


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
2.6453.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.55α = 90
b = 90.55β = 90
c = 56.82γ = 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
11.5556.8299.90.050.9920.29.438608
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)
11.551.5899.61.250.525.6

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 REPLACEMENTTHROUGHOUT1.5556.8236683192399.940.178870.178020.19516RANDOM30
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]
0.260.130.26-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_4_deg24.002
r_dihedral_angle_3_deg12.67
r_long_range_B_refined7.433
r_long_range_B_other7.296
r_scangle_other6.179
r_dihedral_angle_1_deg5.606
r_mcangle_it4.24
r_mcangle_other4.24
r_scbond_it4.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.193
r_dihedral_angle_4_deg24.002
r_dihedral_angle_3_deg12.67
r_long_range_B_refined7.433
r_long_range_B_other7.296
r_scangle_other6.179
r_dihedral_angle_1_deg5.606
r_mcangle_it4.24
r_mcangle_other4.24
r_scbond_it4.186
r_scbond_other4.183
r_angle_other_deg3.727
r_mcbond_it3.001
r_mcbond_other2.97
r_angle_refined_deg2.26
r_chiral_restr0.136
r_bond_refined_d0.027
r_gen_planes_other0.022
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 Atoms1661
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing