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Crystal Structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to Norovirus GII RNA polymerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 160 g/L PEG 8000, 250 g/L Glycerol, 100 mM Tris-Cl, pH 7.0, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM mercaptoethanol, 1 g/L CHAPS, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.6 α = 90 b = 93.7 β = 90 c = 96.6 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD WHITE BEAM SLITS, CRYO-COOLED FIRST AND SAGITTALLY BENT SECOND CRYSTAL OF DOUBLE CRYSTAL MONOCHROMATOR 2008-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.77 20 98.9 0.047 0.047 21 5.94 65879 65879 -3 37.1
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 1.77 1.97 96.5 0.67
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT 3BSO 1.77 19.84 62586 62586 3294 100 0.20745 0.20745 0.20543 0.1979 0.24578 0.2321 RANDOM 34.771
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] 2.16 -1.94 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.776 r_dihedral_angle_4_deg 21.28 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 4.929 r_scangle_it 4.782 r_scbond_it 3.408 r_mcangle_it 2.499 r_mcbond_it 1.556 r_angle_refined_deg 1.074 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.776 r_dihedral_angle_4_deg 21.28 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 4.929 r_scangle_it 4.782 r_scbond_it 3.408 r_mcangle_it 2.499 r_mcbond_it 1.556 r_angle_refined_deg 1.074 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3690 Nucleic Acid Atoms 344 Solvent Atoms 441 Heterogen Atoms 57
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction