3ZSR

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 40MM TRIS PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0M AMMONIUM SULFATE, 100MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5
Crystal Properties
Matthews coefficientSolvent content
2.4550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.778α = 90
b = 70.778β = 90
c = 67.096γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-09-18MSINGLE 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
11.761.399.90.0816.55.741416120.9
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)
11.71.791000.362.15.6

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 3NF71.745.273930920741000.169290.168040.19261RANDOM20.853
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]
0.210.10.21-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.218
r_dihedral_angle_3_deg13.151
r_dihedral_angle_4_deg11.537
r_dihedral_angle_1_deg5.277
r_scangle_it2.877
r_scbond_it1.976
r_mcangle_it1.383
r_angle_refined_deg1.359
r_mcbond_it1.057
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.218
r_dihedral_angle_3_deg13.151
r_dihedral_angle_4_deg11.537
r_dihedral_angle_1_deg5.277
r_scangle_it2.877
r_scbond_it1.976
r_mcangle_it1.383
r_angle_refined_deg1.359
r_mcbond_it1.057
r_nbtor_refined0.307
r_nbd_refined0.22
r_symmetry_vdw_refined0.2
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.117
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
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 Atoms201
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing