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Structure of the receptor-binding protein of bacteriophage Det7: a podoviral tailspike in a myovirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TSP PDB ENTRY 1TSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 10 TO 30 % (W/V) PEG4000, 0.1 M SODIUM CITRATE PH 4.5, 0 TO 15 % (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.433 α = 90 b = 100.433 β = 90 c = 330.042 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 IMAGE PLATE MARRESEARCH SILICON TOROIDAL MIRROR 2004-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 15 94.6 0.08 13.1 5.2 80189 14.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 85.9 0.25 3.8 4.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TSP 1.6 15 78590 1598 94.6 0.142 0.141 0.1552 0.17 RANDOM 13.12
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] 0.95 0.48 0.95 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 13.375 r_dihedral_angle_3_deg 12.264 r_dihedral_angle_1_deg 6.587 r_scangle_it 5.61 r_scbond_it 3.666 r_mcangle_it 2.434 r_angle_refined_deg 1.655 r_mcbond_it 1.418 r_angle_other_deg 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.123 r_dihedral_angle_4_deg 13.375 r_dihedral_angle_3_deg 12.264 r_dihedral_angle_1_deg 6.587 r_scangle_it 5.61 r_scbond_it 3.666 r_mcangle_it 2.434 r_angle_refined_deg 1.655 r_mcbond_it 1.418 r_angle_other_deg 0.888 r_symmetry_vdw_other 0.215 r_nbd_refined 0.196 r_nbd_other 0.183 r_nbtor_refined 0.169 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.121 r_nbtor_other 0.08 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4143 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing