3VQ7

HIV-1 IN core domain in complex with 4-(1H-pyrrol-1-yl)aniline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L3UPDB ENTRY 3l3u

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62951.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.284α = 90
b = 61.658β = 90
c = 82.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMirror2007-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.95363Australian SynchrotronMX1

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
11.634.1599.570.080.0915.27.2385883842222
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6341.69295.74

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3l3u1.6334.153858836498192499.460.1990.200420.1990.22677RANDOM20.482
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]
-0.331.43-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.937
r_dihedral_angle_3_deg14.657
r_dihedral_angle_4_deg13.073
r_dihedral_angle_1_deg5.987
r_scangle_it3.293
r_scbond_it2.293
r_angle_refined_deg1.749
r_mcangle_it1.715
r_mcbond_it1.202
r_angle_other_deg0.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.937
r_dihedral_angle_3_deg14.657
r_dihedral_angle_4_deg13.073
r_dihedral_angle_1_deg5.987
r_scangle_it3.293
r_scbond_it2.293
r_angle_refined_deg1.749
r_mcangle_it1.715
r_mcbond_it1.202
r_angle_other_deg0.959
r_symmetry_vdw_other0.29
r_mcbond_other0.241
r_nbd_refined0.219
r_xyhbond_nbd_refined0.2
r_nbd_other0.199
r_metal_ion_refined0.19
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.177
r_nbtor_refined0.176
r_chiral_restr0.086
r_nbtor_other0.083
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2190
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms61

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling