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Crystal structure of murine norovirus P domain in complex with Nanobody NB-5853
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M Lithium sulfate 0.1 M Sodium acetate pH 4.5 30%(w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.69 α = 90 b = 85.29 β = 113.47 c = 77.97 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 4M 2018-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.96 38.58 98.5 0.143 0.155 0.994 8.97 6.463 61772 28.747
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) Redundancy Number Unique Reflections (All) 1 1.96 2.01 97 0.743 0.808 0.726 2.25 6.437
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 3LQ6 1.96 38.58 58492 3280 98.59 0.2015 0.1989 0.2059 0.2482 0.2534 RANDOM 26.738
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] -0.2 1.06 -1.73 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.837 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 8.22 r_angle_refined_deg 1.548 r_angle_other_deg 1.279 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.837 r_dihedral_angle_4_deg 19.188 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 8.22 r_angle_refined_deg 1.548 r_angle_other_deg 1.279 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6605 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing