4ID1

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ITGPDB ENTRY 1ITG

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
2.7455.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.242α = 90
b = 72.242β = 90
c = 66.148γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2012-09-23MSINGLE 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
11.8762.56399.50.035255169091684533
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)
11.871.91000.4664.6860

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ITG1.8762.561690516784169699.290.19970.19590.2337RANDOM35.9666
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]
0.310.150.31-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.949
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg15.945
r_dihedral_angle_1_deg5.674
r_scangle_it4.242
r_scbond_it2.752
r_mcangle_it2.291
r_angle_refined_deg1.701
r_mcbond_it1.278
r_chiral_restr0.128
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.949
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg15.945
r_dihedral_angle_1_deg5.674
r_scangle_it4.242
r_scbond_it2.752
r_mcangle_it2.291
r_angle_refined_deg1.701
r_mcbond_it1.278
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1100
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms45

Software

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