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Crystal structure of 9-mer peptide from H9N2 avian influenza virus in complex with BF2*0201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M Imidazole pH 7.0, 20% w/v Polyethylene glycol 6,000
Crystal Properties Matthews coefficient Solvent content 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.782 α = 90 b = 76.553 β = 92.449 c = 87.143 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 EIGER2 S 9M 2022-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
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 1.9 43.532 100 0.996 9.1 6.5 65173
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 1.9 1.95 100 0.438 2 5.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 43.532 65152 3321 99.951 0.206 0.2039 0.2118 0.2402 0.2475 39.556
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] -0.5 -0.321 0.233 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.48 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_2_deg 6.879 r_dihedral_angle_1_deg 6.874 r_lrange_it 4.911 r_lrange_other 4.869 r_scangle_it 3.687 r_scangle_other 3.687 r_scbond_it 2.394 r_scbond_other 2.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.48 r_dihedral_angle_3_deg 13.485 r_dihedral_angle_2_deg 6.879 r_dihedral_angle_1_deg 6.874 r_lrange_it 4.911 r_lrange_other 4.869 r_scangle_it 3.687 r_scangle_other 3.687 r_scbond_it 2.394 r_scbond_other 2.394 r_mcangle_it 2.384 r_mcangle_other 2.383 r_angle_refined_deg 1.645 r_mcbond_it 1.588 r_mcbond_other 1.586 r_angle_other_deg 0.592 r_nbd_refined 0.208 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.18 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_other 0.111 r_nbd_other 0.11 r_symmetry_nbd_refined 0.104 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6091 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms
Software Software Software Name Purpose xia2 data reduction xia2 data scaling PHASER phasing REFMAC refinement