6ECO

Hexamer-2-Foldon HIV-1 capsid platform


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52930.2M Sodium Chloride, 0.1M HEPES pH 7.5, 12% PEG 8000
Crystal Properties
Matthew coefficientSolvent content
3.0359.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.25α = 90
b = 95.25β = 90
c = 122.57γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2017-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9798NSLS-II17-ID-1

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
14.250.0194.70.110.9974.438601
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)
14.24.310.90.8151.4

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 REPLACEMENTTHROUGHOUT4XFX4.230469021498.140.287660.286370.31638RANDOM256.555
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]
-12.68-6.34-12.6841.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.166
r_dihedral_angle_4_deg15.074
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg4.601
r_angle_refined_deg1.349
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_sphericity_bonded
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.166
r_dihedral_angle_4_deg15.074
r_dihedral_angle_3_deg11.464
r_dihedral_angle_1_deg4.601
r_angle_refined_deg1.349
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_sphericity_bonded
r_angle_other_deg
r_gen_planes_other
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_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3252
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building