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Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 744-1289 at 2.9 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 294 4-7% (w/v) PEG 6000
100 mM Tris-HCl pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.11 60.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.297 α = 90 b = 76.133 β = 97.62 c = 139.868 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 CCD ADSC QUANTUM 270 2013-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.89 45.18 96.6 0.098 9.4 3.3 48930 69.5
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 2.89 3.04 91.8 0.436 3 3.3
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 5NXF 2.89 45.18 47006 1911 96.47 0.2021 0.19962 0.2058 0.26262 0.2632 RANDOM 64.78
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] -2.68 -7.86 3.05 1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 17.517 r_dihedral_angle_3_deg 16.297 r_long_range_B_refined 10.12 r_long_range_B_other 10.116 r_mcangle_it 7.205 r_mcangle_other 7.205 r_dihedral_angle_1_deg 7.144 r_scangle_other 6.513 r_mcbond_it 4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 17.517 r_dihedral_angle_3_deg 16.297 r_long_range_B_refined 10.12 r_long_range_B_other 10.116 r_mcangle_it 7.205 r_mcangle_other 7.205 r_dihedral_angle_1_deg 7.144 r_scangle_other 6.513 r_mcbond_it 4.5 r_mcbond_other 4.5 r_scbond_it 3.891 r_scbond_other 3.89 r_angle_refined_deg 1.48 r_angle_other_deg 0.979 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12441 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing