2OXO

Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1 M Tris, 0.2 M lithium sulfate, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.693α = 90
b = 46.693β = 90
c = 111.533γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV2006-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
1243.0730.03534.26.7850328.1
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)
22.0774.50.1747.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT243.07765884595.370.234260.228380.28878RANDOM23.913
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.254
r_dihedral_angle_4_deg26.706
r_dihedral_angle_3_deg17.177
r_dihedral_angle_1_deg5.817
r_scangle_it3.735
r_scbond_it2.844
r_mcangle_it1.661
r_angle_refined_deg1.623
r_mcbond_it1.035
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.254
r_dihedral_angle_4_deg26.706
r_dihedral_angle_3_deg17.177
r_dihedral_angle_1_deg5.817
r_scangle_it3.735
r_scbond_it2.844
r_mcangle_it1.661
r_angle_refined_deg1.623
r_mcbond_it1.035
r_nbtor_refined0.298
r_symmetry_vdw_refined0.229
r_nbd_refined0.216
r_xyhbond_nbd_refined0.199
r_chiral_restr0.145
r_symmetry_hbond_refined0.128
r_bond_refined_d0.02
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms708
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing