6AXX

Structure of the T58A/I124A mutant of the HIV-1 capsid protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291PEG3350, NaI, MIB, Glycerol
Crystal Properties
Matthew coefficientSolvent content
2.7455.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.646α = 90
b = 91.646β = 90
c = 57.695γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSRDI CMOS_8M2016-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.000031ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.645.8299.50.1070.1120.0340.99918.310.68617
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.71961.3911.4690.4660.5779.7

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 REPLACEMENTTHROUGHOUT4XFX2.645.8810151299.680.19310.18960.2465RANDOM69.192
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]
-0.02-0.01-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_sphericity_free33.13
r_sphericity_bonded32.167
r_dihedral_angle_4_deg17.618
r_dihedral_angle_3_deg13.513
r_dihedral_angle_1_deg5.899
r_angle_refined_deg1.315
r_angle_other_deg0.931
r_chiral_restr0.061
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_sphericity_free33.13
r_sphericity_bonded32.167
r_dihedral_angle_4_deg17.618
r_dihedral_angle_3_deg13.513
r_dihedral_angle_1_deg5.899
r_angle_refined_deg1.315
r_angle_other_deg0.931
r_chiral_restr0.061
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1658
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms17

Software

Software
Software NamePurpose
Aimlessdata scaling
Blu-Icedata collection
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata reduction
PHASERphasing