3L3U

Crystal structure of the HIV-1 integrase core domain to 1.4A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EXQPDB ENTRY 1exq

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62931.8M Ammonium sulfate, 0.15M sodium citrate, 5mM cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.55α = 90
b = 62.434β = 90
c = 81.127γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.900020APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.434.01599.80.1120.11215.212.5601316013111.1
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)
11.41.481000.4396.613.38679

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1exq1.434.01260063306499.70.2050.2040.236RANDOM11.97
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]
0.41-0.22-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.881
r_dihedral_angle_4_deg20.622
r_dihedral_angle_3_deg13.449
r_scangle_it7.227
r_dihedral_angle_1_deg5.936
r_scbond_it5.075
r_mcangle_it3.246
r_mcbond_it2.198
r_rigid_bond_restr2.139
r_angle_refined_deg2.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.881
r_dihedral_angle_4_deg20.622
r_dihedral_angle_3_deg13.449
r_scangle_it7.227
r_dihedral_angle_1_deg5.936
r_scbond_it5.075
r_mcangle_it3.246
r_mcbond_it2.198
r_rigid_bond_restr2.139
r_angle_refined_deg2.079
r_angle_other_deg1.106
r_mcbond_other0.734
r_chiral_restr0.136
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2263
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms15

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction