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Crystal Structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 286 sodium potassium tartrate, ADA, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties Matthews coefficient Solvent content 4.01 69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.395 α = 90 b = 88.395 β = 90 c = 186.198 γ = 120
Symmetry Space Group P 32 2 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 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 2.5 20 0.095 0.095 17 7.7 30009 30009
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) 2.5 2.6 99 0.055 0.055 4.4 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 20 28454 28456 1520 99.94 0.23031 0.22859 0.2626 RANDOM 31.391
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] 1.79 0.89 1.79 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.331 r_dihedral_angle_4_deg 19.953 r_dihedral_angle_1_deg 5.472 r_scangle_it 1.95 r_angle_refined_deg 1.121 r_scbond_it 1.096 r_mcangle_it 0.929 r_angle_other_deg 0.779 r_mcbond_it 0.481 r_symmetry_vdw_other 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.331 r_dihedral_angle_4_deg 19.953 r_dihedral_angle_1_deg 5.472 r_scangle_it 1.95 r_angle_refined_deg 1.121 r_scbond_it 1.096 r_mcangle_it 0.929 r_angle_other_deg 0.779 r_mcbond_it 0.481 r_symmetry_vdw_other 0.226 r_nbd_other 0.217 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.143 r_metal_ion_refined 0.091 r_nbtor_other 0.085 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_3_deg r_nbtor_refined r_xyhbond_nbd_other 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 3688 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement