6OBH

Structure of HIV-1 CA 1/2-hexamer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H47PDB entry 3H47

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH82930.1 M PCB buffer, pH 8 (sodium propionate, sodium cacodylate, Bis-Tris propane), 25% w/v PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.77α = 70.65
b = 77.746β = 70.7
c = 77.758γ = 70.59
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.964592.50.0514.91.83053299.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.963.0186.030.3510.9

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 REPLACEMENTTHROUGHOUTPDB entry 3H472.964529060147192.490.210990.2080.26469RANDOM103.954
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]
1.053.981.860.422.732.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.551
r_dihedral_angle_4_deg21.917
r_long_range_B_other20
r_long_range_B_refined19.999
r_dihedral_angle_3_deg17.085
r_mcangle_other15.646
r_mcangle_it15.645
r_scangle_other14.775
r_mcbond_it10.208
r_mcbond_other10.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.551
r_dihedral_angle_4_deg21.917
r_long_range_B_other20
r_long_range_B_refined19.999
r_dihedral_angle_3_deg17.085
r_mcangle_other15.646
r_mcangle_it15.645
r_scangle_other14.775
r_mcbond_it10.208
r_mcbond_other10.201
r_scbond_it9.369
r_scbond_other9.369
r_dihedral_angle_1_deg7.332
r_angle_refined_deg1.437
r_angle_other_deg1.186
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms10061
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIXrefinement