8QUY | pdb_00008quy

Hexameric HIV-1 CA in complex with DDD01728501


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HGM 

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
2.6653.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.76α = 90
b = 90.76β = 90
c = 57γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2017-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.8845.3899.90.090.9912.45.421682
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)
11.881.9198.11.030.521.64.6

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 REPLACEMENTTHROUGHOUT1.8845.3820638104098.950.181170.179460.190.215240.22RANDOM30.399
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]
0.020.010.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.059
r_dihedral_angle_4_deg22.513
r_dihedral_angle_3_deg14.554
r_long_range_B_refined7.708
r_long_range_B_other7.706
r_scangle_other6.13
r_dihedral_angle_1_deg6.116
r_mcangle_it4.329
r_mcangle_other4.329
r_scbond_it4.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.059
r_dihedral_angle_4_deg22.513
r_dihedral_angle_3_deg14.554
r_long_range_B_refined7.708
r_long_range_B_other7.706
r_scangle_other6.13
r_dihedral_angle_1_deg6.116
r_mcangle_it4.329
r_mcangle_other4.329
r_scbond_it4.18
r_scbond_other4.174
r_mcbond_it3.039
r_mcbond_other3.03
r_angle_refined_deg1.979
r_angle_other_deg1.136
r_chiral_restr0.136
r_bond_refined_d0.023
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.002
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 Atoms1660
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing