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Structure of the carboxy-terminal domain of the bacteriophage T5 L- shaped tail fiber with its intra-molecular chaperone domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UW7 PDB ENTRY 4UW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 10 MM TRIS-HCL, 0.1 M SODIUM CITRATE PH 4.0, 12.5 % (W/V) PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.8 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.85 α = 90 b = 99.29 β = 91.51 c = 286.23 γ = 90
Symmetry Space Group C 1 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 VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION 2013-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.52 95.4 98.8 0.14 6.3 4.1 150772 48.4
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 2.52 2.65 97.2 0.43 3.5 3.8
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4UW7 2.52 95.38 148385 2061 98.47 0.18497 0.18455 0.1901 0.21311 0.2184 THIN SHELLS 43.689
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] 0.65 0.53 -0.15 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 14.046 r_dihedral_angle_3_deg 13.996 r_dihedral_angle_1_deg 6.808 r_scangle_it 4.944 r_mcangle_it 4.137 r_scbond_it 3.097 r_mcbond_it 2.661 r_mcbond_other 2.66 r_angle_refined_deg 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 14.046 r_dihedral_angle_3_deg 13.996 r_dihedral_angle_1_deg 6.808 r_scangle_it 4.944 r_mcangle_it 4.137 r_scbond_it 3.097 r_mcbond_it 2.661 r_mcbond_other 2.66 r_angle_refined_deg 1.397 r_angle_other_deg 1.1 r_symmetry_vdw_refined 0.306 r_symmetry_vdw_other 0.246 r_nbd_refined 0.209 r_nbd_other 0.178 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_other 0.143 r_symmetry_hbond_refined 0.136 r_symmetry_hbond_other 0.136 r_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 27442 Nucleic Acid Atoms Solvent Atoms 936 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing