6ES8

HIV capsid hexamer with IP6 ligand


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE277PEG4K
Crystal Properties
Matthew coefficientSolvent content
2.8156.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.299α = 90
b = 91.299β = 90
c = 57.201γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDOXFORD RUBY CCD2017-01-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.97991.50.08410.84.621569
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9294.10.8780.9431.64.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5HGP1.946.391879096791.610.187630.185730.22372RANDOM36.23
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]
-0.1-0.05-0.10.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.84
r_dihedral_angle_4_deg22.485
r_dihedral_angle_3_deg14.734
r_long_range_B_refined8.081
r_long_range_B_other8.031
r_scangle_other6.521
r_dihedral_angle_1_deg5.712
r_scbond_other4.342
r_scbond_it4.334
r_mcangle_it4.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.84
r_dihedral_angle_4_deg22.485
r_dihedral_angle_3_deg14.734
r_long_range_B_refined8.081
r_long_range_B_other8.031
r_scangle_other6.521
r_dihedral_angle_1_deg5.712
r_scbond_other4.342
r_scbond_it4.334
r_mcangle_it4.247
r_mcangle_other4.245
r_mcbond_it3.108
r_mcbond_other3.107
r_angle_refined_deg1.931
r_angle_other_deg1.172
r_chiral_restr0.48
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1580
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing