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Crystal structure of RNA dependent RNA polymerase domain from west nile virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HCS WEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10% peg 8000,
Imid 0.1M,
Ca(OAc)2 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.04 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.064 α = 90 b = 110.064 β = 90 c = 68.572 γ = 90
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 2005-11-27 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 2.35 69 99.9 0.055 21.8 5.7 34338 61.1
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 2.35 2.48 99.7 0.56 1.5 3.5 4930
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 WEST NILE VIRUS RNA DEPENDANT RNA POLYMERASE COORDINATES 2HCS (DOMAIN FROM AMINO ACIDS 317-905) 2.35 34.82 34348 32583 1734 99.92 0.20962 0.20962 0.20701 0.2036 0.25944 0.2555 RANDOM 58.568
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] -1.96 -1.96 3.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_3_deg 20.655 r_dihedral_angle_4_deg 19.044 r_dihedral_angle_1_deg 7.286 r_scangle_it 2.747 r_scbond_it 1.827 r_angle_refined_deg 1.729 r_mcangle_it 1.255 r_mcbond_it 0.728 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.388 r_dihedral_angle_3_deg 20.655 r_dihedral_angle_4_deg 19.044 r_dihedral_angle_1_deg 7.286 r_scangle_it 2.747 r_scbond_it 1.827 r_angle_refined_deg 1.729 r_mcangle_it 1.255 r_mcbond_it 0.728 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.257 r_nbd_refined 0.216 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.151 r_metal_ion_refined 0.022 r_bond_refined_d 0.021 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3931 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction AMoRE phasing