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Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor PPNDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 1.2M sodium citrate, 0.1M sodium cacodylate, 0.125M sodium chloride, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.75 α = 90 b = 116.1 β = 90 c = 122.09 γ = 90
Symmetry Space Group I 2 2 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 PIXEL PSI PILATUS 6M 2013-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 38.4 99.6 19046 19046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.66 99.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.6 38.4 18061 18061 985 99.61 0.22321 0.21993 0.2218 0.28535 0.2861 RANDOM 57.007
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] 1.5 -1.33 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.657 r_dihedral_angle_4_deg 17.803 r_dihedral_angle_3_deg 15.791 r_dihedral_angle_1_deg 5.522 r_angle_other_deg 3.538 r_angle_refined_deg 1.183 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.657 r_dihedral_angle_4_deg 17.803 r_dihedral_angle_3_deg 15.791 r_dihedral_angle_1_deg 5.522 r_angle_other_deg 3.538 r_angle_refined_deg 1.183 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 Atoms Number Protein Atoms 3880 Nucleic Acid Atoms 46 Solvent Atoms 132 Heterogen Atoms 157
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling