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Crystal structure of human respiratory syncytial virus NS1 bound to human MED25 ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VJ2 experimental model PDB 2L23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.15 M ammonium tartrate, 0.1 M MES pH 5.6, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.953 α = 90 b = 104.953 β = 90 c = 63.45 γ = 90
Symmetry Space Group P 43 21 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 PILATUS3 2M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00002 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 50 100 0.073 0.996 54 25 12815
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.0475
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 (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 2.53 48.23 10304 537 87.92 0.24343 0.24246 0.2454 0.26211 0.2653 RANDOM 41.322
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] -0.4 -0.4 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.232 r_dihedral_angle_1_deg 6.588 r_long_range_B_refined 4.013 r_long_range_B_other 4.013 r_dihedral_angle_2_deg 3.697 r_mcangle_it 2.446 r_mcangle_other 2.446 r_scangle_other 1.369 r_mcbond_it 1.295 r_mcbond_other 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.232 r_dihedral_angle_1_deg 6.588 r_long_range_B_refined 4.013 r_long_range_B_other 4.013 r_dihedral_angle_2_deg 3.697 r_mcangle_it 2.446 r_mcangle_other 2.446 r_scangle_other 1.369 r_mcbond_it 1.295 r_mcbond_other 1.295 r_angle_refined_deg 0.805 r_scbond_it 0.645 r_scbond_other 0.645 r_angle_other_deg 0.277 r_chiral_restr 0.035 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2137 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing