5J1P

Lassa virus L protein cap-snatching endonuclease. Bound to two manganese ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72972mM MnCl, 5mM DPBA, 5 mM MgCl chloride hexahydrate, 0.05 M HEPES-Na pH7 25 % (v/v) PEG MME 550
Crystal Properties
Matthews coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.42α = 90
b = 51.42β = 90
c = 144.18γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2011-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.976SOLEILPROXIMA 1

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
12.3648.4399.80.064226.78543
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)
12.362.461.208

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 REPLACEMENTTHROUGHOUT5J1N2.3648.43809344199.840.208190.203740.28861RANDOM64.561
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]
-1.48-1.482.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_4_deg18.165
r_sphericity_free13.955
r_dihedral_angle_3_deg13.641
r_sphericity_bonded13.423
r_dihedral_angle_1_deg6.058
r_long_range_B_refined4.942
r_scbond_it3.943
r_mcangle_it3.825
r_mcbond_it3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_4_deg18.165
r_sphericity_free13.955
r_dihedral_angle_3_deg13.641
r_sphericity_bonded13.423
r_dihedral_angle_1_deg6.058
r_long_range_B_refined4.942
r_scbond_it3.943
r_mcangle_it3.825
r_mcbond_it3.04
r_angle_refined_deg1.47
r_rigid_bond_restr1.342
r_chiral_restr0.099
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
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_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1363
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing