3JU0

Structure of the arm-type binding domain of HAI7 integrase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32770.1M MES, pH6.3, 2.8M ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5351.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.53α = 90
b = 52.53β = 90
c = 79.47γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirror2009-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0015SLSX10SA

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
11.6691.60.02730.67164711508922
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)
11.61.7760.1079.31

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)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 3JTZ1.662164711411375092.280.150650.147570.21211RANDOM23.278
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]
0.350.170.35-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.512
r_dihedral_angle_1_deg19.108
r_dihedral_angle_4_deg17.33
r_dihedral_angle_3_deg16.217
r_sphericity_free11.306
r_scangle_it7.255
r_sphericity_bonded5.754
r_scbond_it4.916
r_mcangle_it3.695
r_rigid_bond_restr2.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.512
r_dihedral_angle_1_deg19.108
r_dihedral_angle_4_deg17.33
r_dihedral_angle_3_deg16.217
r_sphericity_free11.306
r_scangle_it7.255
r_sphericity_bonded5.754
r_scbond_it4.916
r_mcangle_it3.695
r_rigid_bond_restr2.458
r_mcbond_it2.42
r_angle_refined_deg2.051
r_mcbond_other1.163
r_angle_other_deg0.814
r_chiral_restr0.12
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d0.002
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_metal_ion_refined
r_xyhbond_nbd_refined
r_nbtor_other
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_gen_planes_other
r_xyhbond_nbd_other
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms737
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling