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The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Sodium Bromide, 20% PEG 3350, 0.1M Bis-Tris propane, 0.1% chymotrypsin, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.39 α = 90 b = 114.42 β = 90 c = 120.22 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2013-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 1.8 82.88 100 0.062 10.2 4.2 83310 83310 2 2 33.8
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 1.8 1.83 96.4 0.234 2.8 4 4379
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3U43 1.8 82.88 2.3 83310 79092 4150 98.81 0.17372 0.17372 0.17155 0.1823 0.21514 0.2242 RANDOM 29.381
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] 0.45 -1.08 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.183 r_dihedral_angle_4_deg 18.315 r_dihedral_angle_3_deg 16.688 r_long_range_B_refined 7.682 r_long_range_B_other 7.452 r_dihedral_angle_1_deg 5.96 r_scangle_other 4.666 r_mcangle_it 2.967 r_mcangle_other 2.967 r_scbond_it 2.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.183 r_dihedral_angle_4_deg 18.315 r_dihedral_angle_3_deg 16.688 r_long_range_B_refined 7.682 r_long_range_B_other 7.452 r_dihedral_angle_1_deg 5.96 r_scangle_other 4.666 r_mcangle_it 2.967 r_mcangle_other 2.967 r_scbond_it 2.963 r_scbond_other 2.963 r_mcbond_it 1.991 r_mcbond_other 1.989 r_angle_refined_deg 1.773 r_angle_other_deg 0.869 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 6856 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 39
Software Software Software Name Purpose EDNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling