4CEF

Interrogating HIV integrase for compounds that bind- a SAMPL challenge


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZSQPDB ENTRY 3ZSQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5THE 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
2.9558

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.565α = 90
b = 70.565β = 90
c = 66.612γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian 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
11.761.11000.0814.95.5408381
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)
11.71.791000.423.25.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZSQ1.745.0438765204399.990.16940.167760.20019RANDOM21.389
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]
0.170.080.17-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.356
r_dihedral_angle_3_deg13.386
r_dihedral_angle_4_deg8.735
r_dihedral_angle_1_deg5.297
r_scangle_it2.878
r_scbond_it1.885
r_mcangle_it1.421
r_angle_refined_deg1.359
r_mcbond_it0.885
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.356
r_dihedral_angle_3_deg13.386
r_dihedral_angle_4_deg8.735
r_dihedral_angle_1_deg5.297
r_scangle_it2.878
r_scbond_it1.885
r_mcangle_it1.421
r_angle_refined_deg1.359
r_mcbond_it0.885
r_nbtor_refined0.308
r_nbd_refined0.228
r_symmetry_vdw_refined0.212
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.102
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms152
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing