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Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 286 ammonium sulfate, citrate, AMPPNP, MgCl2 or MnCl2, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 2.85 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.976 α = 90 b = 100.955 β = 90 c = 116.839 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 ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.3 20 0.074 0.074 15 5.2 53177 53177
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.4 99 0.342 0.342 5.5 5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 20 50371 50371 2700 99.29 0.25664 0.25442 0.29702 RANDOM 28.106
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] 1.8 -0.49 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.872 r_dihedral_angle_4_deg 24.302 r_dihedral_angle_1_deg 5.582 r_scangle_it 1.846 r_angle_refined_deg 1.114 r_scbond_it 1.07 r_mcangle_it 0.899 r_angle_other_deg 0.795 r_mcbond_it 0.471 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.872 r_dihedral_angle_4_deg 24.302 r_dihedral_angle_1_deg 5.582 r_scangle_it 1.846 r_angle_refined_deg 1.114 r_scbond_it 1.07 r_mcangle_it 0.899 r_angle_other_deg 0.795 r_mcbond_it 0.471 r_nbtor_refined 0.303 r_nbd_other 0.214 r_symmetry_vdw_other 0.214 r_nbd_refined 0.18 r_symmetry_hbond_refined 0.177 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.138 r_nbtor_other 0.085 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_3_deg r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7364 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement