X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BISPDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)
experimental modelPDB 1Z9EPDB Entry: 1BIS (Integrase), 1Z9E (LEDGF)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.25295PEG-3350, Na2HPO4, NaH2PO4, KH2PO4, NACL, HEPES, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1241.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.421α = 90
b = 60.593β = 109.06
c = 71.126γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.00NSLSX26C

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
12.025099.20.07218.94.832648321363.13.135.2
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)
12.022.0999.299.20.473.14.5

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: 1BIS (Integrase), 1Z9E (LEDGF)2.02203040632113162799.190.1830.1830.1810.226RANDOM37.386
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]
0.031.3-0.381.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.69
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg5.524
r_scangle_it4.361
r_scbond_it2.778
r_angle_refined_deg1.602
r_mcangle_it1.6
r_mcbond_it0.981
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.69
r_dihedral_angle_4_deg19.538
r_dihedral_angle_3_deg15.922
r_dihedral_angle_1_deg5.524
r_scangle_it4.361
r_scbond_it2.778
r_angle_refined_deg1.602
r_mcangle_it1.6
r_mcbond_it0.981
r_nbtor_refined0.301
r_symmetry_hbond_refined0.237
r_nbd_refined0.213
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.147
r_chiral_restr0.132
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3503
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms34

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
CCP4phasing