7M0N

The crystal structure of wild type PA endonuclease (A/Vietnam/1203/2004) in complex with Raltegravir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911.5M ammonium sulfate, 2% PEG1500, 0.1 M Tris pH 8.0, and 1 mM MnCl2. then overnight crystals soak in 1.65 M ammonium sulfate, 2% PEG1500, 0.1 M Tris pH 8.0, 5 mM MnCl2, 10 mM MnCl2 and 20mM Raltegravir.
Crystal Properties
Matthews coefficientSolvent content
3.1460.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.702α = 90
b = 135.126β = 90
c = 126.751γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2012-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97999APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.446.2299.60.0960.0520.0370.99610.67.44260753.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4996.80.6470.7180.3030.7711.94.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4E5F2.442.441.3442524209999.360.19350.19150.231473.85
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.6207
f_angle_d0.5275
f_chiral_restr0.0391
f_plane_restr0.0038
f_bond_d0.0024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5962
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms206

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing