3ZT4

Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NF7PDB ENTRY 3NF7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
Crystal Properties
Matthews coefficientSolvent content
2.4550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.058α = 90
b = 71.058β = 90
c = 66.559γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.261.551000.1510.45.7191321
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321000.82.15.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3NF72.261.54181089811000.173360.170410.2293RANDOM29.731
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]
0.040.020.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.069
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg15.583
r_dihedral_angle_1_deg5.99
r_angle_refined_deg2.105
r_angle_other_deg1.404
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.069
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg15.583
r_dihedral_angle_1_deg5.99
r_angle_refined_deg2.105
r_angle_other_deg1.404
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2335
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing