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Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with protein primer VPg and a pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CDU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 293 2M ammonium sulfate, 0.1M CAPS, 0.2M lithium sulfate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.53 65.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.213 α = 90 b = 74.213 β = 90 c = 285.591 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 MAR CCD 165 mm 2006-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.9330 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 27.45 99.9 0.084 17 6.45 28820 28791 2 2 56.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 99.7 0.386 2.6 4
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 MOLECULAR REPLACEMENT THROUGHOUT 3CDU 2.5 27.45 28765 27251 1451 99.78 0.1829 0.1829 0.1753 0.1813 0.2196 0.2188 RANDOM 41.3
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] -4.34454516 -4.34454516 8.68909033
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 18.852 t_it 1.304 t_angle_deg 1.041 t_nbd 0.026 t_gen_planes 0.01 t_bond_d 0.008 t_trig_c_planes 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3819 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 202
Software Software Software Name Purpose BUSTER-TNT refinement ADSC data collection MOSFLM data reduction SCALA data scaling AMoRE phasing