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Tailspike protein double mutant D339N/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 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.257 α = 90 b = 74.257 β = 90 c = 174.512 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 1.5 43.14 99.9 0.073 0.032 0.999 18.4 6 90151
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 1.5 1.53 98 0.743 0.364 0.731 2.1 5.1 4325
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 1.5 43.14 90151 4504 99.95 0.1438 0.1425 0.142 0.1685 0.1679 RANDOM 15.108
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] 0.19 0.1 0.19 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.337 r_dihedral_angle_4_deg 16.845 r_dihedral_angle_3_deg 11.345 r_dihedral_angle_1_deg 7.445 r_angle_refined_deg 1.795 r_mcangle_it 0.96 r_angle_other_deg 0.916 r_mcbond_it 0.668 r_mcbond_other 0.668 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.337 r_dihedral_angle_4_deg 16.845 r_dihedral_angle_3_deg 11.345 r_dihedral_angle_1_deg 7.445 r_angle_refined_deg 1.795 r_mcangle_it 0.96 r_angle_other_deg 0.916 r_mcbond_it 0.668 r_mcbond_other 0.668 r_chiral_restr 0.125 r_bond_refined_d 0.019 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 746 Heterogen Atoms 98
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