4O55

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277.510% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion,hanging drop, temperature 277.5K
Crystal Properties
Matthews coefficientSolvent content
2.754.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.73α = 90
b = 71.73β = 90
c = 65.943γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2013-03-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.541

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
12.262.1299.70.04218.64.7102971028733
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)
12.22.241000.5844.7514

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2462.129766969446199.250.17840.17510.2588RANDOM68.121
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]
0.980.490.98-3.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.121
r_dihedral_angle_3_deg20.841
r_dihedral_angle_4_deg13.466
r_dihedral_angle_1_deg6.438
r_scbond_it4.749
r_mcangle_it4.043
r_mcbond_it2.781
r_angle_refined_deg1.809
r_chiral_restr0.102
r_bond_refined_d0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.121
r_dihedral_angle_3_deg20.841
r_dihedral_angle_4_deg13.466
r_dihedral_angle_1_deg6.438
r_scbond_it4.749
r_mcangle_it4.043
r_mcbond_it2.781
r_angle_refined_deg1.809
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1092
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms48

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling