3NF6

Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.32931.7M ammonium sulfate, 0.1M sodium acetate pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4649.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.488α = 90
b = 71.488β = 90
c = 66.819γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95660Australian 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
11.945.499.960.073301211.126.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9299.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.930.962858328583151099.970.18050.18050.179020.20783RANDOM27.492
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]
0.160.080.16-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.7
r_dihedral_angle_3_deg14.041
r_dihedral_angle_4_deg12.813
r_dihedral_angle_1_deg5.681
r_scangle_it3.139
r_scbond_it2.172
r_angle_refined_deg1.706
r_mcangle_it1.691
r_mcbond_it1.079
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.7
r_dihedral_angle_3_deg14.041
r_dihedral_angle_4_deg12.813
r_dihedral_angle_1_deg5.681
r_scangle_it3.139
r_scbond_it2.172
r_angle_refined_deg1.706
r_mcangle_it1.691
r_mcbond_it1.079
r_nbtor_refined0.302
r_nbd_refined0.221
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.143
r_chiral_restr0.09
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2318
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms138

Software

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