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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, 10% (v/v) isopropanol, N-nonylphosphocholine (FOS-CHOLINE-9 from Hampton screen 3, No. 18), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.165 α = 90 b = 57.165 β = 90 c = 195.385 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 APS BEAMLINE 17-ID 1.0 APS 17-ID
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 1.9 34.77 99.3 0.054 0.054 44 7.1 30054 30054 32
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 1.9 2 98.6 0.398 0.398 3.6 6.7 2912
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 Monomer from 1ZH1 1.9 34.77 29345 29345 626 99.26 0.248 0.248 0.247 0.2443 0.288 0.2846 RANDOM 33.996
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 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.421 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 15.961 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.413 r_scbond_it 1.615 r_angle_refined_deg 1.222 r_mcangle_it 1.201 r_mcbond_it 0.699 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.421 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 15.961 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.413 r_scbond_it 1.615 r_angle_refined_deg 1.222 r_mcangle_it 1.201 r_mcbond_it 0.699 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.225 r_symmetry_hbond_refined 0.199 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.086 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 254 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing