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Tailspike protein mutant E372Q of E. coli bacteriophage HK620 in complex with pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris-HCl, 3.5 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.16 42.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.179 α = 90 b = 74.179 β = 90 c = 174.678 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 PIXEL DECTRIS PILATUS 6M mirrors 2014-01-28 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 1.06 43.67 99.4 0.058 0.028 0.999 13.9 5.2 250525
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 1.06 1.08 89 0.62 0.357 0.694 2.1 3.7 10927
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XM3 1.06 43.67 250525 12512 99.27 0.1065 0.1053 0.1065 0.1296 0.1299 RANDOM 11.576
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] 0.27 0.13 0.27 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_sphericity_free 35.774 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 10.658 r_sphericity_bonded 10.087 r_dihedral_angle_1_deg 7.658 r_rigid_bond_restr 6.01 r_angle_refined_deg 1.938 r_mcangle_it 1.788 r_mcbond_it 1.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_sphericity_free 35.774 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 10.658 r_sphericity_bonded 10.087 r_dihedral_angle_1_deg 7.658 r_rigid_bond_restr 6.01 r_angle_refined_deg 1.938 r_mcangle_it 1.788 r_mcbond_it 1.393 r_mcbond_other 1.392 r_angle_other_deg 0.978 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4532 Nucleic Acid Atoms Solvent Atoms 852 Heterogen Atoms 103
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC phasing ARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction