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Structure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (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 3.5 293 0.2M Li(SO4), 0.1M Na citrate pH 3.5, 28% (v/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.97 58.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.73 α = 90 b = 155.73 β = 90 c = 161.88 γ = 120
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 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97934 ESRF ID23-1
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 2.28 49 95 0.096 0.099 0.023 0.998 19.8 19.5 28985
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 2.28 2.435 2.623 2.699 0.891 0.323
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 2.28 28.42 28965 1487 84 0.183 0.181 0.1897 0.213 0.2199 RANDOM 80.83
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] 1.0434 1.0434 -2.0868
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.16 t_omega_torsion 3.32 t_angle_deg 1.16 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 17.16 t_omega_torsion 3.32 t_angle_deg 1.16 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 3562 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 53
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing