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Structure of Zika virus NS3 helicase in complex with ADP-BeF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 20% w/v glycerol, 10% w/v polyethylene glycol 4000, 0.1 M MES/imidazole pH 6.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, and 20 mM sodium potassium L-tartrate.
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.92 α = 90 b = 71.36 β = 93.73 c = 57.349 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 PIXEL DECTRIS PILATUS 6M-F 2016-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.7 57.23 99.4 0.065 0.999 13.1 4.1 46828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 94.3 1.508 0.444 1 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JLQ 1.7 57.23 44518 2312 99.37 0.169 0.167 0.1771 0.206 0.2138 RANDOM 33.142
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.934 r_dihedral_angle_4_deg 14.592 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 6.174 r_angle_refined_deg 1.54 r_angle_other_deg 0.959 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.934 r_dihedral_angle_4_deg 14.592 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 6.174 r_angle_refined_deg 1.54 r_angle_other_deg 0.959 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3450 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction