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Crystal structure of the Zika virus NS3 helicase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 292 Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.05M Tris-HCl pH=8.5; JCSG+ B12: 0.2 M tri-Potassium citrate, 20 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.639 α = 90 b = 69.855 β = 93.41 c = 58.461 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD C(111) 2016-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 2.05 30 98.1 0.073 0.073 17.7 4.5 25603 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 97.2 0.635 0.724 2.3 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 5JRZ 2.05 29.97 24316 1271 97.93 0.18706 0.18421 0.24674 0.2692 RANDOM 45.902
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] -0.72 0.28 -0.65 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.448 r_dihedral_angle_3_deg 11.656 r_dihedral_angle_4_deg 10.969 r_long_range_B_refined 5.297 r_long_range_B_other 5.251 r_scangle_other 3.492 r_dihedral_angle_1_deg 3.072 r_mcangle_it 2.928 r_mcangle_other 2.927 r_scbond_it 2.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.448 r_dihedral_angle_3_deg 11.656 r_dihedral_angle_4_deg 10.969 r_long_range_B_refined 5.297 r_long_range_B_other 5.251 r_scangle_other 3.492 r_dihedral_angle_1_deg 3.072 r_mcangle_it 2.928 r_mcangle_other 2.927 r_scbond_it 2.132 r_scbond_other 2.131 r_mcbond_other 1.853 r_mcbond_it 1.852 r_angle_refined_deg 1.398 r_angle_other_deg 0.84 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3426 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing