6LMI

Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LPT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1M Sodium cacodylate pH6.5, 0.32M Ammonium sulfate, 9% PEG 8000, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.6753.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.926α = 90
b = 71.926β = 90
c = 65.798γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2012-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.55086.60.0988.94.76189
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)
12.52.5490.90.5744.4

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 REPLACEMENTTHROUGHOUT3LPT2.520587028086.690.19960.19740.2439RANDOM45.794
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]
0.20.10.2-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.608
r_dihedral_angle_3_deg18.689
r_dihedral_angle_4_deg15.133
r_dihedral_angle_1_deg5.448
r_angle_refined_deg1.355
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1065
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms64

Software

Software
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootdata reduction