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Crystal structure of tailspike depolymerase (APK14_gp49) from Acinetobacter phage vB_AbaP_APK14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 50mM CaCl2, 100mM Bis-tris pH 6.5, 30%PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.394 α = 90 b = 77.394 β = 90 c = 228.536 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 EIGER X 16M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 1.55 228.54 100 0.145 0.15 0.039 0.999 7.7 15.3 111761
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 1.55 1.58 100 2.706 2.83 0.819 0.431 11.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.55 114.27 106071 5588 99.93 0.20141 0.19951 0.2138 0.23574 0.2146 RANDOM 26.268
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] -0.09 -0.04 -0.09 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.659 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 8.644 r_long_range_B_refined 5.719 r_long_range_B_other 5.703 r_scangle_other 5.031 r_scbond_it 3.693 r_scbond_other 3.693 r_mcangle_it 3.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.659 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 8.644 r_long_range_B_refined 5.719 r_long_range_B_other 5.703 r_scangle_other 5.031 r_scbond_it 3.693 r_scbond_other 3.693 r_mcangle_it 3.462 r_mcangle_other 3.461 r_mcbond_it 2.796 r_mcbond_other 2.795 r_angle_refined_deg 2.103 r_angle_other_deg 1.541 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.015 r_bond_other_d 0.003 r_gen_planes_other 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 5494 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction CRANK2 phasing PDB_EXTRACT data extraction