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Crystal structure of tailspike depolymerase (APK09_gp48) from Acinetobacter phage APK09
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 7.5 288 2% PEG200, 100mM HEPES pH 7.5, 20% tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.688 α = 90 b = 88.688 β = 90 c = 421.04 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 6M 2021-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 ESRF ID23-1
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 2.59 72.15 99.1 0.339 0.349 0.081 0.993 10.9 18.5 20409
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 2.59 2.7 94 2.467 2.566 0.674 0.303 13.6
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 2.59 72.15 19304 1052 99.26 0.19312 0.18867 0.1886 0.27157 0.2717 RANDOM 58.755
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] 0.68 0.34 0.68 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.93 r_dihedral_angle_3_deg 20.901 r_dihedral_angle_4_deg 19.604 r_long_range_B_refined 13 r_dihedral_angle_1_deg 10.17 r_mcangle_it 9.961 r_scbond_it 9.171 r_mcbond_it 7.508 r_angle_refined_deg 2.379 r_chiral_restr 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.93 r_dihedral_angle_3_deg 20.901 r_dihedral_angle_4_deg 19.604 r_long_range_B_refined 13 r_dihedral_angle_1_deg 10.17 r_mcangle_it 9.961 r_scbond_it 9.171 r_mcbond_it 7.508 r_angle_refined_deg 2.379 r_chiral_restr 0.173 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4588 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction