6XW5

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5820


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LQ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29125% PEG3000, 0.1M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.72α = 90
b = 101.72β = 90
c = 228.52γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.072270ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.7249.8699.90.0660.069122.3413.01912787630.811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.76990.7910.8240.9353.0412.457

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 REPLACEMENTTHROUGHOUT3LQ61.7249.86121577629999.860.16290.16140.1911RANDOM27.631
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]
1.081.08-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.586
r_dihedral_angle_4_deg20.136
r_dihedral_angle_3_deg12.074
r_dihedral_angle_1_deg7.61
r_angle_refined_deg1.735
r_angle_other_deg1.464
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.586
r_dihedral_angle_4_deg20.136
r_dihedral_angle_3_deg12.074
r_dihedral_angle_1_deg7.61
r_angle_refined_deg1.735
r_angle_other_deg1.464
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6484
Nucleic Acid Atoms
Solvent Atoms712
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing