7D83

Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-(2-(3-cyclohexylureido)-3,6-dimethyl-5-(5-methylchroman-6-yl)pyridin-4-yl)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LMQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.1M Sodium cacodylate pH 6.5, 0.2M Ammonium sulfate, 1% PEG 8000, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.754.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.312α = 90
b = 72.312β = 90
c = 65.845γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5

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
12.4362.6299.80.08310.86.57819
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)
12.432.4796.80.565.6

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 REPLACEMENTTHROUGHOUT6LMQ2.4362.62744435999.860.22630.22390.2779RANDOM53.344
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]
0.840.420.84-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.824
r_dihedral_angle_4_deg16.848
r_dihedral_angle_3_deg16.329
r_dihedral_angle_1_deg5.184
r_angle_refined_deg1.043
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1088
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms53

Software

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