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Crystal structure of a tailspike depolymerase (Belisarius_gp86) from Acinetobacter phage Belisarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 Bis-tris pH 5.5, 2.4M NaCl
Crystal Properties Matthews coefficient Solvent content 5.87 79.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.975 α = 90 b = 100.975 β = 90 c = 784.525 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 2M 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977180 LNLS SIRIUS MANACA
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 2.2 49.67 99.9 0.305 0.317 0.084 0.957 8.2 14.4 79321
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 2.2 2.24 100 1.936 2.007 0.523 0.75 14.5
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 2.2 49.67 75166 3993 99.64 0.21119 0.2104 0.216 0.2261 0.2293 RANDOM 49.898
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] -0.37 -0.18 -0.37 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.137 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 9.72 r_long_range_B_other 9.552 r_long_range_B_refined 9.551 r_mcangle_it 8.797 r_mcangle_other 8.797 r_scangle_other 8.777 r_scbond_it 6.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.137 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_1_deg 9.72 r_long_range_B_other 9.552 r_long_range_B_refined 9.551 r_mcangle_it 8.797 r_mcangle_other 8.797 r_scangle_other 8.777 r_scbond_it 6.426 r_scbond_other 6.425 r_mcbond_it 6.338 r_mcbond_other 6.337 r_angle_refined_deg 1.924 r_angle_other_deg 1.361 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 4379 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing