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Structure of the C-terminal domain of bacteriophage K gp155, native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9F49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3 294 15% (w/v) PEG 8000, 83 mM MES-NaOH, 10 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.13 α = 90 b = 43.334 β = 94.084 c = 98.982 γ = 90
Symmetry Space Group P 1 21 1
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 2018-11-28 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) 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 1.52 62.38 95.5 0.063 0.076 0.042 0.996 8.4 2.9 95840 22.2
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 1.52 1.6 0.647 0.802 0.466 0.652 1.4
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 1.52 62.38 95832 4666 95.309 0.189 0.1881 0.1971 0.2131 0.2216 24.003
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] 0.392 0.743 -0.542 0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.448 r_dihedral_angle_4_deg 13.436 r_dihedral_angle_3_deg 12.824 r_dihedral_angle_1_deg 6.665 r_lrange_it 5.474 r_lrange_other 5.219 r_scangle_it 3.276 r_scangle_other 3.275 r_mcangle_it 2.16 r_mcangle_other 2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.448 r_dihedral_angle_4_deg 13.436 r_dihedral_angle_3_deg 12.824 r_dihedral_angle_1_deg 6.665 r_lrange_it 5.474 r_lrange_other 5.219 r_scangle_it 3.276 r_scangle_other 3.275 r_mcangle_it 2.16 r_mcangle_other 2.16 r_scbond_it 2.071 r_scbond_other 2.071 r_mcbond_it 1.395 r_mcbond_other 1.394 r_angle_refined_deg 1.316 r_angle_other_deg 1.313 r_symmetry_nbd_refined 0.323 r_nbd_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_other 0.16 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.142 r_nbd_other 0.124 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3724 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing