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Phage epsilon15 tailspike gp20 containing domains beta-helix, beta-sandwich and petal domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LW3 experimental model PDB 9SIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M Tris-HcL pH 7.5, 3 M Na-formate
Crystal Properties Matthews coefficient Solvent content 3.61 65.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.326 α = 90 b = 117.326 β = 90 c = 251.291 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 2018-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 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 1.94 83.904 96.3 0.998 10.3 5.1 92011 29.276066
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 1.94 2.04 75.6 0.647 1.6 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.94 83.904 92009 4737 96.318 0.16 0.1592 0.163 0.1782 0.182 32.057
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] -0.253 -0.126 -0.253 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.929 r_dihedral_angle_3_deg 9.981 r_dihedral_angle_1_deg 6.822 r_dihedral_angle_2_deg 5.161 r_lrange_it 4.612 r_lrange_other 4.422 r_scangle_it 2.241 r_scangle_other 2.241 r_mcangle_it 1.662 r_mcangle_other 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.929 r_dihedral_angle_3_deg 9.981 r_dihedral_angle_1_deg 6.822 r_dihedral_angle_2_deg 5.161 r_lrange_it 4.612 r_lrange_other 4.422 r_scangle_it 2.241 r_scangle_other 2.241 r_mcangle_it 1.662 r_mcangle_other 1.662 r_scbond_it 1.349 r_scbond_other 1.349 r_mcbond_it 0.986 r_mcbond_other 0.986 r_angle_refined_deg 0.88 r_angle_other_deg 0.342 r_nbd_refined 0.189 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.166 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.106 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6305 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing