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Phage epsilon15 tailspike gp20 esterase domain with a fragment of the Salmonella Anatum O-antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 20 mM Tris H-Cl, 100 mM KCl, 0.1 M HEPES pH 7.0, 12% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.85 33.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.475 α = 90 b = 49.703 β = 90 c = 144.418 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2018-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97980 ALBA XALOC
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 2.085 144.42 95.6 0.994 10 10.4 17754 25.21
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 2.085 2.2 78.8 0.599 1.9 5.3
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 2.085 72.209 17697 878 95.525 0.188 0.1863 0.1916 0.2298 0.2321 24.373
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] -0.401 -1.734 2.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.282 r_dihedral_angle_6_deg 14.467 r_dihedral_angle_3_deg 10.827 r_dihedral_angle_1_deg 5.868 r_lrange_it 3.406 r_lrange_other 3.294 r_scangle_it 1.883 r_scangle_other 1.883 r_mcangle_other 1.464 r_mcangle_it 1.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.282 r_dihedral_angle_6_deg 14.467 r_dihedral_angle_3_deg 10.827 r_dihedral_angle_1_deg 5.868 r_lrange_it 3.406 r_lrange_other 3.294 r_scangle_it 1.883 r_scangle_other 1.883 r_mcangle_other 1.464 r_mcangle_it 1.462 r_scbond_it 1.167 r_scbond_other 1.167 r_angle_refined_deg 1.042 r_mcbond_it 0.92 r_mcbond_other 0.916 r_angle_other_deg 0.381 r_chiral_restr 0.217 r_nbd_refined 0.194 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.172 r_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.151 r_symmetry_nbd_refined 0.079 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing