3AO5

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, 0.15M Na Citrate pH 4.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0339.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.032α = 90
b = 49.032β = 90
c = 103.724γ = 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
11.850.8990.0550.0623.15.62590325633
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)
1.81.91000.2640.2944.94.9

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 3L3U1.834.572590324362128399.160.245580.243310.28898RANDOM24.804
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]
0.850.430.85-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.402
r_dihedral_angle_3_deg15.796
r_dihedral_angle_4_deg15.598
r_dihedral_angle_1_deg5.3
r_scangle_it4.805
r_scbond_it3.795
r_mcangle_it3.417
r_mcbond_it2.592
r_angle_refined_deg1.493
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.402
r_dihedral_angle_3_deg15.796
r_dihedral_angle_4_deg15.598
r_dihedral_angle_1_deg5.3
r_scangle_it4.805
r_scbond_it3.795
r_mcangle_it3.417
r_mcbond_it2.592
r_angle_refined_deg1.493
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms2108
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms93

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement