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Dengue 2 Virus NS2B-NS3 protease fusion protein with crystal epitope mutation K174Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 LFS Eco well C09
0.1M HEPES pH 7, 0.2M
Lithium chloride,
20% w/v PEG 6000,
10% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.486 α = 90 b = 45.2 β = 109.108 c = 40.46 γ = 90
Symmetry Space Group C 1 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 EIGER X 16M 2024-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976269 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 42.15 99.86 0.999 10 6.8 15533
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 0.357
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.95 42.148 15533 800 99.852 0.229 0.2257 0.2259 0.2939 0.294 RANDOM 53.484
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] -0.249 -0.097 0.131 0.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.798 r_dihedral_angle_2_deg 17.341 r_dihedral_angle_6_deg 17.111 r_lrange_other 13.604 r_lrange_it 13.6 r_scangle_it 11.573 r_scangle_other 11.568 r_dihedral_angle_1_deg 9.404 r_mcangle_it 8.596 r_mcangle_other 8.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.798 r_dihedral_angle_2_deg 17.341 r_dihedral_angle_6_deg 17.111 r_lrange_other 13.604 r_lrange_it 13.6 r_scangle_it 11.573 r_scangle_other 11.568 r_dihedral_angle_1_deg 9.404 r_mcangle_it 8.596 r_mcangle_other 8.593 r_scbond_it 8.489 r_scbond_other 8.484 r_mcbond_it 6.575 r_mcbond_other 6.56 r_angle_refined_deg 2.72 r_angle_other_deg 1.22 r_symmetry_xyhbond_nbd_refined 0.203 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.156 r_symmetry_nbd_other 0.144 r_nbd_other 0.141 r_chiral_restr 0.138 r_symmetry_nbd_refined 0.086 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1483 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing