6XW4

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5867


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911.0 M Lithium chloride 0.1 M Citric acid pH 5.0 20%(w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
3.1761.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.33α = 90
b = 109.04β = 90
c = 146.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2018-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97856ESRFID30B

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
12.1947.3899.40.1380.150.99610.116.5036225434.419
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)
12.192.2592.50.7530.8210.8482.566.239

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 REPLACEMENTTHROUGHOUT3LQ62.1947.3859137311899.340.17560.17340.2184RANDOM30.375
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]
3.43-1.36-2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg16.127
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg8.283
r_angle_refined_deg1.618
r_angle_other_deg1.282
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg16.127
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg8.283
r_angle_refined_deg1.618
r_angle_other_deg1.282
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6518
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing