3AO1

Fragment-based approach to the design of ligands targeting a novel site in 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 DROP5.62931.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.587α = 90
b = 61.997β = 90
c = 81.765γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm platedouble crystal monochromator and K-B pair of biomorph mirrors2007-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97937APS23-ID-B

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
11.96299.90.0860.0931172497224930
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)
1.921000.480.523.27

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 3L3U1.949.42493023602123499.670.218760.216350.2676RANDOM38.818
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]
-0.332.64-2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.015
r_dihedral_angle_3_deg14.597
r_dihedral_angle_4_deg12.575
r_dihedral_angle_1_deg4.863
r_scangle_it4.325
r_mcangle_it3.119
r_scbond_it3.05
r_mcbond_it2.152
r_angle_refined_deg1.374
r_symmetry_hbond_refined0.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.015
r_dihedral_angle_3_deg14.597
r_dihedral_angle_4_deg12.575
r_dihedral_angle_1_deg4.863
r_scangle_it4.325
r_mcangle_it3.119
r_scbond_it3.05
r_mcbond_it2.152
r_angle_refined_deg1.374
r_symmetry_hbond_refined0.386
r_metal_ion_refined0.254
r_symmetry_vdw_other0.249
r_nbd_refined0.204
r_nbd_other0.186
r_mcbond_other0.184
r_xyhbond_nbd_refined0.181
r_nbtor_refined0.175
r_symmetry_vdw_refined0.114
r_nbtor_other0.083
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_xyhbond_nbd_other0.004
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2159
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms39

Software

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