3AO3

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L3UPDB ENTRY 3l3u

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62931.8M AmSO4, 0.15 M Na Citrate pH 4.6, 5 mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49α = 90
b = 49β = 90
c = 103.6γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2008-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.957Australian SynchrotronMX1

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
11.95096.80.0410.04626.65.7219302122232.6
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)
1.9291.80.2880.3186.25.72860

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3l3u1.939.27212222073210921000.181220.178110.24111RANDOM29.28
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]
1.30.651.3-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_3_deg15.482
r_dihedral_angle_4_deg11.441
r_dihedral_angle_1_deg6.044
r_scangle_it5.173
r_scbond_it3.274
r_mcangle_it2.604
r_angle_refined_deg2.075
r_mcbond_it1.461
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.951
r_dihedral_angle_3_deg15.482
r_dihedral_angle_4_deg11.441
r_dihedral_angle_1_deg6.044
r_scangle_it5.173
r_scbond_it3.274
r_mcangle_it2.604
r_angle_refined_deg2.075
r_mcbond_it1.461
r_chiral_restr0.17
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2087
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms72

Software

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