7QDF

Hexameric HIV-1 (M-group) CA R120 mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XFX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52939.5% PEG 3350 (v/v), 310 mM NaI, 100 mM Sodium Cacodylate. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.
Crystal Properties
Matthews coefficientSolvent content
2.7555.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.36α = 90
b = 92.36β = 90
c = 57.44γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2020-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X131.0332EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.30479.9898.40.0710.99710.763.912346
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)
12.3042.440.5031

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4XFX2.30446.6561227657898.3970.2440.24230.277593.332
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]
-5.699-5.69911.398
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.959
r_dihedral_angle_4_deg24.062
r_dihedral_angle_3_deg20.023
r_lrange_it14.589
r_scangle_it9.558
r_mcangle_it8.903
r_scbond_it6.813
r_mcbond_it6.147
r_dihedral_angle_1_deg5.43
r_angle_refined_deg2.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.959
r_dihedral_angle_4_deg24.062
r_dihedral_angle_3_deg20.023
r_lrange_it14.589
r_scangle_it9.558
r_mcangle_it8.903
r_scbond_it6.813
r_mcbond_it6.147
r_dihedral_angle_1_deg5.43
r_angle_refined_deg2.017
r_symmetry_xyhbond_nbd_refined0.449
r_symmetry_nbd_refined0.405
r_nbtor_refined0.331
r_nbd_refined0.301
r_xyhbond_nbd_refined0.235
r_chiral_restr0.141
r_gen_planes_refined0.01
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1723
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing