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Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GJN PDB entry 3GJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 292 30% PEG 400, 0.1 CHES pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.161 α = 90 b = 67.371 β = 90 c = 123.231 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 CCD MARMOSAIC 225 mm CCD Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 50 95.3 0.13 0.12 8.7 5.9 23137 43.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.24 95.8 0.426 0.334 2 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3GJN 2.2 50 21370 21366 1147 95.41 0.24139 0.23956 0.268 0.27683 0.3142 RANDOM 42.751
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] -3.1 5.2 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.161 r_dihedral_angle_3_deg 23.441 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_1_deg 10.27 r_scangle_it 7.245 r_scbond_it 4.994 r_angle_refined_deg 3.856 r_mcangle_it 3.198 r_mcbond_it 1.914 r_nbtor_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.161 r_dihedral_angle_3_deg 23.441 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_1_deg 10.27 r_scangle_it 7.245 r_scbond_it 4.994 r_angle_refined_deg 3.856 r_mcangle_it 3.198 r_mcbond_it 1.914 r_nbtor_refined 0.36 r_symmetry_vdw_refined 0.351 r_nbd_refined 0.35 r_chiral_restr 0.274 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.157 r_metal_ion_refined 0.142 r_bond_refined_d 0.048 r_gen_planes_refined 0.019 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3213 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling