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Tailspike protein double mutant D339N/E372A of E. coli bacteriophage HK620 in complex with pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris-HCl, 3.5 M Sodiumformiate
Crystal Properties Matthews coefficient Solvent content 2.16 42.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.279 α = 90 b = 74.279 β = 90 c = 174.726 γ = 120
Symmetry Space Group P 3 2 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 CCD RAYONIX MX-225 mirrors 2012-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 43.17 93.9 0.055 0.026 0.999 21 4.9 53810
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 78.3 0.282 0.148 0.92 4.9 3.5 2429
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AVZ 1.75 43.17 53810 2687 93.87 0.1404 0.1385 0.1748 0.1726 RANDOM 14.864
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] 0.25 0.12 0.25 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 16.018 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 7.586 r_angle_refined_deg 1.74 r_mcangle_it 0.92 r_angle_other_deg 0.89 r_mcbond_it 0.604 r_mcbond_other 0.604 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.941 r_dihedral_angle_4_deg 16.018 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 7.586 r_angle_refined_deg 1.74 r_mcangle_it 0.92 r_angle_other_deg 0.89 r_mcbond_it 0.604 r_mcbond_other 0.604 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4543 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 84
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing ARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction