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Lassa virus L protein cap-snatching endonuclease. Bound to two manganese ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 2mM MnCl, 5mM DPBA, 5 mM MgCl chloride hexahydrate,
0.05 M HEPES-Na pH7
25 % (v/v) PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.42 α = 90 b = 51.42 β = 90 c = 144.18 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 300K 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.976 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.36 48.43 99.8 0.064 22 6.7 8543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.46 1.208
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5J1N 2.36 48.43 8093 441 99.84 0.20819 0.20374 0.2036 0.28861 0.289 RANDOM 64.561
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 -1.48 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.504 r_dihedral_angle_4_deg 18.165 r_sphericity_free 13.955 r_dihedral_angle_3_deg 13.641 r_sphericity_bonded 13.423 r_dihedral_angle_1_deg 6.058 r_long_range_B_refined 4.942 r_scbond_it 3.943 r_mcangle_it 3.825 r_mcbond_it 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.504 r_dihedral_angle_4_deg 18.165 r_sphericity_free 13.955 r_dihedral_angle_3_deg 13.641 r_sphericity_bonded 13.423 r_dihedral_angle_1_deg 6.058 r_long_range_B_refined 4.942 r_scbond_it 3.943 r_mcangle_it 3.825 r_mcbond_it 3.04 r_angle_refined_deg 1.47 r_rigid_bond_restr 1.342 r_chiral_restr 0.099 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 1363 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing