3ZSZ

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 5.5 MG/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 = 71.475α = 90
b = 71.475β = 90
c = 66.453γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-07-29MSINGLE 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
1245.31000.0816.45.625674127.12
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)
122.111000.5535.6

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 3NF7231.482434513031000.188420.186570.22221RANDOM26.833
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]
0.180.090.18-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.371
r_dihedral_angle_4_deg16.892
r_dihedral_angle_3_deg14.779
r_dihedral_angle_1_deg6.036
r_scangle_it3.678
r_scbond_it2.588
r_mcangle_it1.795
r_angle_refined_deg1.618
r_mcbond_it1.363
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.371
r_dihedral_angle_4_deg16.892
r_dihedral_angle_3_deg14.779
r_dihedral_angle_1_deg6.036
r_scangle_it3.678
r_scbond_it2.588
r_mcangle_it1.795
r_angle_refined_deg1.618
r_mcbond_it1.363
r_nbtor_refined0.301
r_nbd_refined0.236
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.154
r_chiral_restr0.101
r_symmetry_hbond_refined0.076
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms96
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing