6AXY

Structure of the V11I/T58A/I124A mutant of the HIV-1 capsid protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291PEG3350, NaI, Sodium cacodylate, Glycerol
Crystal Properties
Matthew coefficientSolvent content
2.7655.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.915α = 90
b = 91.915β = 90
c = 57.919γ = 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
12.7845.9697.30.1090.1150.0350.9991810.66969
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)
12.782.9397.31.051.1060.3450.7549.9

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 REPLACEMENTTHROUGHOUTpdbid 4XFX2.7845.96657638397.140.21560.21310.26RANDOM74.506
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]
-0.39-0.19-0.391.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.873
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg12.558
r_dihedral_angle_1_deg5.467
r_angle_refined_deg1.085
r_angle_other_deg0.852
r_chiral_restr0.054
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.873
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg12.558
r_dihedral_angle_1_deg5.467
r_angle_refined_deg1.085
r_angle_other_deg0.852
r_chiral_restr0.054
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1680
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms16

Software

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