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Structure of the post-fusion complex between precursor membrane ectodomain (prM) and envelope ectodomain protein (E) from tick-borne encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URZ 1URZ, 3C5X experimental model PDB 3C5X 1URZ, 3C5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 0.1M Na Malonate, 0.1M HEPES pH 6.7, 18.9% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.935 α = 90 b = 97.935 β = 90 c = 115.164 γ = 120
Symmetry Space Group P 3 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 PIXEL DECTRIS PILATUS3 6M 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 2.8 48.97 98.9 0.238 0.286 0.117 0.99 6.3 5.7 15904
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 2.8 2.95 2.73 3.25 1.31 0.306
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 1URZ, 3C5X 2.8 48.97 15902 826 98.2 0.23 0.228 0.2571 0.264 0.299 RANDOM 79.9
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] -13.7134 -13.7134 27.4269
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.88 t_omega_torsion 1.73 t_angle_deg 0.93 t_bond_d 0.007 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 18.88 t_omega_torsion 1.73 t_angle_deg 0.93 t_bond_d 0.007 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 3642 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 12
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing