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Crystal structure of a novel dimeric form of HCV NS5A domain I protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZH1 Monomer from 1ZH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 22% PEG-3350, 0.1 M HEPES pH 7.5, and 10% (v/v) isopropanol; 2,6-dimethyl-4-heptyl-beta-D-maltopyranoside (Hampton detergent screen 2, No. 3), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.106 α = 90 b = 57.106 β = 90 c = 197.365 γ = 120
Symmetry Space Group P 31 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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.2 50 99.2 0.108 0.108 17.7 6.2 19703 19703 34.7
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) 1 2.2 2.25 92 0.535 0.535 2 4 1163
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Monomer from 1ZH1 2.2 50 19213 19213 406 99.12 0.2223 0.2223 0.22162 0.25534 0.2271 RANDOM 29.786
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] 0.4 0.2 0.4 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.391 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 16.953 r_dihedral_angle_1_deg 5.65 r_scangle_it 2.461 r_scbond_it 1.54 r_angle_refined_deg 1.237 r_mcangle_it 1.158 r_mcbond_it 0.664 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.391 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 16.953 r_dihedral_angle_1_deg 5.65 r_scangle_it 2.461 r_scbond_it 1.54 r_angle_refined_deg 1.237 r_mcangle_it 1.158 r_mcbond_it 0.664 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2466 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing