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Structure of the hetero-tetramer complex between precursor membrane protein fragment (pr) and envelope protein (E) from tick-borne encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVB 1SVB, 3C5X experimental model PDB 3C5X 1SVB, 3C5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.2M (NH4)SO4, 0.1M Na acetate pH 4.6, 28% (v/v) PEG MME 550, 2.8% (v/v) tert-Butanol
Crystal Properties Matthews coefficient Solvent content 3.01 59.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.32 α = 90 b = 164.32 β = 90 c = 164.32 γ = 90
Symmetry Space Group P 41 3 2
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 2018-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.07197 SOLEIL PROXIMA 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 2.7 49.56 100 0.244 0.248 0.043 0.998 13.8 32.9 21401 101.65
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 2.7 2.83 100 4.825 4.908 0.89 0.332 30
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 1SVB, 3C5X 2.7 49.54 21399 1071 99.9 0.191 0.188 0.1994 0.249 0.259 RANDOM 85.14
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 t_other_torsion 19.3 t_omega_torsion 3.17 t_angle_deg 1.26 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.3 t_omega_torsion 3.17 t_angle_deg 1.26 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3658 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 48
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction