2XI7

N-terminal endonuclease domain of La Crosse virus L-protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XI5PDB ENTRY 2XI5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.515-20 MG/ML PROTEIN IN 20 MM HEPES PH 7.5 150 MM NACL 5MM MNCL2 AND 2.5 MM BETA-MERCAPTO-ETHANOL AND A RESERVOIR COMPOSITION OF 3.4 M NA-FORMATE 0.1 M TRIS-HCL PH 8
Crystal Properties
Matthews coefficientSolvent content
469.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.59α = 90
b = 124.59β = 90
c = 294.71γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.2501000.0823.414.369332
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)
12.22.281000.595.114.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XI52.247.296652327871000.190.1880.221RANDOM26.06
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]
0.480.240.48-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.52
r_dihedral_angle_3_deg15.021
r_dihedral_angle_4_deg14.741
r_dihedral_angle_1_deg5.477
r_scangle_it4.883
r_scbond_it2.884
r_mcangle_it1.886
r_angle_refined_deg1.556
r_mcbond_it0.958
r_angle_other_deg0.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.52
r_dihedral_angle_3_deg15.021
r_dihedral_angle_4_deg14.741
r_dihedral_angle_1_deg5.477
r_scangle_it4.883
r_scbond_it2.884
r_mcangle_it1.886
r_angle_refined_deg1.556
r_mcbond_it0.958
r_angle_other_deg0.932
r_mcbond_other0.212
r_chiral_restr0.095
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6116
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing