8QUW

Hexameric HIV-1 CA in complex with DDD01044153


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HGM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52900.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN
Crystal Properties
Matthews coefficientSolvent content
2.6353.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.472α = 90
b = 90.472β = 90
c = 56.688γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2017-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.0228.3498.50.120.99115.817180
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)
12.022.1389.70.470.7934.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0228.341628887098.680.191330.189260.23048RANDOM25.968
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]
0.310.160.31-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.469
r_dihedral_angle_4_deg21.848
r_dihedral_angle_3_deg13.773
r_long_range_B_refined6.201
r_long_range_B_other6.201
r_dihedral_angle_1_deg5.773
r_scangle_other4.285
r_angle_other_deg3.692
r_mcangle_it3.605
r_mcangle_other3.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.469
r_dihedral_angle_4_deg21.848
r_dihedral_angle_3_deg13.773
r_long_range_B_refined6.201
r_long_range_B_other6.201
r_dihedral_angle_1_deg5.773
r_scangle_other4.285
r_angle_other_deg3.692
r_mcangle_it3.605
r_mcangle_other3.603
r_scbond_it2.8
r_scbond_other2.8
r_mcbond_it2.473
r_mcbond_other2.465
r_angle_refined_deg1.77
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_other0.013
r_gen_planes_refined0.009
r_bond_other_d
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 Atoms1664
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing