☰ Navigation Tabs
X-ray crystallographic structure of the NS3 helicase domain from Tick-borne encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Crystals were initially identified in the Morpheus II screen condition G5 (15% PEG 3K, 20% 1,2,4 butanetriol, 1% NDSB-256, 20 mM arginine, 20 mM threonine, 20 mM histidine, 20 mM hydroxylysine, 20 mM trans-4-hydroxy-L-proline, and buffered by 50 mM BES and 50 mM triethanolamine at pH 7.5). Seeds were generated from this condition and used for random microseed matrix screening (rMMS) using a protein concentration of 10-12 mg/ml. Final crystals were identified in the Index HT screen condition H2 (0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3,350). Crystals were cryoprotected by transfer to a drop containing a 4:1 ratio of precipitant ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.787 α = 90 b = 55.442 β = 93.75 c = 91.267 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 EIGER X 9M 2019-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920089 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.95 45.55 99.5 0.123 0.135 0.053 0.986 7.7 6.1 31169
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 93.7 0.28 0.327 0.162 0.453 4.2
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 5GJC 1.95 45.55 29614 1523 99.45 0.1841 0.1821 0.1906 0.2237 0.2312 RANDOM 26.02
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] 1.16 1.36 -2.97 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.36 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 13.281 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.632 r_angle_other_deg 1.371 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.36 r_dihedral_angle_4_deg 17.739 r_dihedral_angle_3_deg 13.281 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.632 r_angle_other_deg 1.371 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction