3ZT0

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 = 71.355α = 90
b = 71.355β = 90
c = 67.08γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2009-07-29MSINGLE 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
11.9545.451000.0718.55.627877125.77
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)
11.952.061000.443.75.6

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 3NF71.9545.4526328139899.550.205040.203150.24004RANDOM25.553
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]
0.440.220.44-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.925
r_dihedral_angle_4_deg17.396
r_dihedral_angle_3_deg15.33
r_dihedral_angle_1_deg6.329
r_scangle_it3.391
r_scbond_it2.446
r_mcangle_it1.839
r_angle_refined_deg1.797
r_mcbond_it1.247
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.925
r_dihedral_angle_4_deg17.396
r_dihedral_angle_3_deg15.33
r_dihedral_angle_1_deg6.329
r_scangle_it3.391
r_scbond_it2.446
r_mcangle_it1.839
r_angle_refined_deg1.797
r_mcbond_it1.247
r_nbtor_refined0.302
r_nbd_refined0.221
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.157
r_chiral_restr0.116
r_symmetry_hbond_refined0.069
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2318
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing