8QUJ | pdb_00008quj

Hexameric HIV-1 CA in complex with DDD00100452


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
2.6553.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.685α = 90
b = 90.685β = 90
c = 56.763γ = 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
11.6356.891.30.060.9919.59.630451
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)
11.631.63596.50.990.6928.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6356.828974147591.220.178140.1770.190.199710.21RANDOM31.142
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]
0.150.070.15-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.712
r_dihedral_angle_4_deg24.957
r_dihedral_angle_3_deg14.377
r_long_range_B_refined7.669
r_long_range_B_other7.667
r_dihedral_angle_1_deg6.535
r_scangle_other5.377
r_mcangle_other3.81
r_mcangle_it3.805
r_angle_other_deg3.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.712
r_dihedral_angle_4_deg24.957
r_dihedral_angle_3_deg14.377
r_long_range_B_refined7.669
r_long_range_B_other7.667
r_dihedral_angle_1_deg6.535
r_scangle_other5.377
r_mcangle_other3.81
r_mcangle_it3.805
r_angle_other_deg3.802
r_scbond_it3.655
r_scbond_other3.653
r_mcbond_it2.642
r_mcbond_other2.631
r_angle_refined_deg1.983
r_chiral_restr0.095
r_gen_planes_other0.018
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms1701
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing