3OVN

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 DROP5.62931.6M AmSO4, 0.1M Na Citrate pH 5.6, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.75α = 90
b = 59.704β = 90
c = 81.818γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors2007-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1APS23-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
11.9548.2599.40.10.1129.74.5232032181122.38
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)
1.952.0699.40.4970.4792.94.63184

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 3L3U1.9540.912181120602111798.830.212780.210840.24882RANDOM25.036
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]
-0.833.24-2.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_3_deg16.86
r_dihedral_angle_4_deg11.879
r_dihedral_angle_1_deg6.585
r_scangle_it4.472
r_scbond_it2.897
r_angle_refined_deg2.174
r_mcangle_it2.124
r_mcbond_it1.189
r_angle_other_deg1.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_3_deg16.86
r_dihedral_angle_4_deg11.879
r_dihedral_angle_1_deg6.585
r_scangle_it4.472
r_scbond_it2.897
r_angle_refined_deg2.174
r_mcangle_it2.124
r_mcbond_it1.189
r_angle_other_deg1.062
r_mcbond_other0.277
r_chiral_restr0.112
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2168
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms61

Software

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