8QVA | pdb_00008qva

Hexameric HIV-1 CA in complex with DDD01829894


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
2.6152.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.343α = 90
b = 90.343β = 90
c = 56.424γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2018-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
1239.1297.60.080.9910.33.217458
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)
122.0599.30.420.6933.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT239.121658687097.550.205230.202540.210.254340.26RANDOM27.343
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]
0.230.120.23-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.205
r_dihedral_angle_4_deg14.79
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.932
r_long_range_B_other6.705
r_dihedral_angle_1_deg6.37
r_scangle_other4.406
r_mcangle_it3.939
r_mcangle_other3.938
r_scbond_it2.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.205
r_dihedral_angle_4_deg14.79
r_dihedral_angle_3_deg13.795
r_long_range_B_refined6.932
r_long_range_B_other6.705
r_dihedral_angle_1_deg6.37
r_scangle_other4.406
r_mcangle_it3.939
r_mcangle_other3.938
r_scbond_it2.858
r_scbond_other2.856
r_mcbond_it2.507
r_mcbond_other2.497
r_angle_refined_deg1.773
r_angle_other_deg1.056
r_chiral_restr0.103
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1677
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing