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Crystal structure of P domain from GII.11 swine norovirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100mM Tris (pH 8.0), 16% (w/v) polyethylene glycol 3350, 6% (v/v) tacsimate (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.237 α = 90 b = 76.237 β = 90 c = 241.799 γ = 90
Symmetry Space Group P 43 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 CCD ADSC QUANTUM 315r 2014-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.0000 SSRF BL17U1
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 1.998 50 99.9 0.14 30 8.7 49356
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 2.09 100 0.489 8.3
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 3PUN 2 50 46779 2497 99.65 0.18154 0.17974 0.188 0.21627 0.223 RANDOM 22.866
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] -0.86 -0.86 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.508 r_dihedral_angle_4_deg 19.204 r_dihedral_angle_3_deg 10.546 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 4.932 r_long_range_B_other 4.439 r_scangle_other 2.405 r_mcangle_it 1.999 r_mcangle_other 1.999 r_scbond_it 1.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.508 r_dihedral_angle_4_deg 19.204 r_dihedral_angle_3_deg 10.546 r_dihedral_angle_1_deg 6.425 r_long_range_B_refined 4.932 r_long_range_B_other 4.439 r_scangle_other 2.405 r_mcangle_it 1.999 r_mcangle_other 1.999 r_scbond_it 1.445 r_scbond_other 1.444 r_angle_refined_deg 1.211 r_mcbond_it 1.206 r_mcbond_other 1.206 r_angle_other_deg 0.794 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4741 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing