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Crystal structure of 9-mer peptide from ALV-J in complex with BF2*0201
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 1.0 M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.614 α = 90 b = 115.584 β = 111.158 c = 94.107 γ = 90
Symmetry Space Group P 1 21 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 1.72 115.58 98.9 0.993 11.2 3.3 180693
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 1.72 1.76 0.507 2.3
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 1.72 87.763 180502 8875 98.721 0.184 0.1821 0.1915 0.2123 0.2203 18.963
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] -0.001 -0.001 -0.002 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.58 r_dihedral_angle_3_deg 14.675 r_lrange_it 7.041 r_lrange_other 6.961 r_dihedral_angle_2_deg 6.881 r_dihedral_angle_1_deg 6.76 r_scangle_it 5.084 r_scangle_other 5.084 r_scbond_it 3.22 r_scbond_other 3.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.58 r_dihedral_angle_3_deg 14.675 r_lrange_it 7.041 r_lrange_other 6.961 r_dihedral_angle_2_deg 6.881 r_dihedral_angle_1_deg 6.76 r_scangle_it 5.084 r_scangle_other 5.084 r_scbond_it 3.22 r_scbond_other 3.219 r_mcangle_it 3.156 r_mcangle_other 3.156 r_mcbond_it 2.129 r_mcbond_other 2.129 r_angle_refined_deg 1.511 r_angle_other_deg 0.527 r_symmetry_nbd_refined 0.308 r_nbd_refined 0.207 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.183 r_nbd_other 0.182 r_symmetry_xyhbond_nbd_other 0.178 r_xyhbond_nbd_refined 0.167 r_ncsr_local_group_7 0.099 r_ncsr_local_group_1 0.098 r_ncsr_local_group_6 0.098 r_ncsr_local_group_8 0.098 r_ncsr_local_group_11 0.095 r_ncsr_local_group_3 0.094 r_ncsr_local_group_2 0.089 r_ncsr_local_group_10 0.086 r_ncsr_local_group_4 0.085 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_12 0.084 r_ncsr_local_group_9 0.083 r_ncsr_local_group_5 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12179 Nucleic Acid Atoms Solvent Atoms 1440 Heterogen Atoms
Software Software Software Name Purpose DIALS data reduction DIALS data scaling PHASER phasing REFMAC refinement