3WNF

Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62931.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5MM CADMIUM CHLORIDE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.07α = 90
b = 50.07β = 90
c = 102.57γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2009-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.954Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.455094.40.0380.04322.75.55103948158263341
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.586.10.4260.4713.75.523206

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3L3U1.4543.36510394770325111000.200560.19890.23226RANDOM17.128
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]
0.930.470.93-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg14.627
r_dihedral_angle_4_deg10.151
r_dihedral_angle_1_deg6.722
r_scangle_it6.093
r_scbond_it3.749
r_mcangle_it2.749
r_angle_refined_deg2.437
r_mcbond_it1.734
r_angle_other_deg1.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.235
r_dihedral_angle_3_deg14.627
r_dihedral_angle_4_deg10.151
r_dihedral_angle_1_deg6.722
r_scangle_it6.093
r_scbond_it3.749
r_mcangle_it2.749
r_angle_refined_deg2.437
r_mcbond_it1.734
r_angle_other_deg1.116
r_mcbond_other0.463
r_chiral_restr0.135
r_bond_refined_d0.029
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2161
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms36

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling