4OVL | pdb_00004ovl

Interrogating HIV integrase for compounds that bind- a SAMPL challenge


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293THE PROTEIN WAS CONCENTRATED TO 5.5 MG/ML IN 40 mM TRIS PH 8.0, 250 mM NACL, 30 mM MGCL2, 5 mM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 mM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.
Crystal Properties
Matthews coefficientSolvent content
2.4850.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.492α = 90
b = 71.492β = 90
c = 67.357γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRON0.95661Australian SynchrotronMX1

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
11.745.699.90.074145.642336
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)
11.71.790.75325

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.745.6240069213799.660.200170.199380.20720.214780.223RANDOM26.766
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]
0.030.030.03-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.281
r_dihedral_angle_3_deg13.497
r_dihedral_angle_4_deg8.144
r_long_range_B_refined6.011
r_long_range_B_other6.01
r_dihedral_angle_1_deg5.065
r_scangle_other3.309
r_mcangle_it2.979
r_mcangle_other2.978
r_scbond_it2.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.281
r_dihedral_angle_3_deg13.497
r_dihedral_angle_4_deg8.144
r_long_range_B_refined6.011
r_long_range_B_other6.01
r_dihedral_angle_1_deg5.065
r_scangle_other3.309
r_mcangle_it2.979
r_mcangle_other2.978
r_scbond_it2.008
r_scbond_other2.007
r_mcbond_it1.707
r_mcbond_other1.699
r_angle_refined_deg1.404
r_angle_other_deg0.753
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2318
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement