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Crystal Structure of Hepatitis C Virus IRES Subdomain IIa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PN3 PDB ENTRY 2PN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.2 290 30% MPD, 80mM SrCl2, 25mM NaCl, 50mM Cacodylate equilibrated with 60%MPD, pH 6.2, EVAPORATION, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.286 α = 90 b = 48.73 β = 90 c = 119.999 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 77 CCD ADSC QUANTUM 315 mirrors 2006-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM 0.97949 APS 8-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.32 59.98 95.9 0.108 17.5 5.5 12751 12228 59.9
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 2.32 2.43 100 0.714 2.4 6.9 1247
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 PDB ENTRY 2PN3 2.32 59.98 12210 11590 598 94.92 0.26515 0.26405 0.26141 0.2571 0.32037 0.3228 RANDOM 51.272
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] -2.24 -0.38 2.62
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.94 r_angle_refined_deg 1.835 r_scbond_it 1.409 r_symmetry_hbond_refined 0.317 r_nbtor_refined 0.279 r_metal_ion_refined 0.222 r_nbd_refined 0.165 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.94 r_angle_refined_deg 1.835 r_scbond_it 1.409 r_symmetry_hbond_refined 0.317 r_nbtor_refined 0.279 r_metal_ion_refined 0.222 r_nbd_refined 0.165 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1860 Solvent Atoms 67 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing