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Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMV PDB ENTRY 1EMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 277 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.903 α = 90 b = 88.248 β = 91.92 c = 52.235 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 4 2000-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 20 96.3 0.027 34.4 51260 51260 1 1
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) 1.6 1.66 84.5 0.045 4468
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1EMV 1.6 19.86 3 53245 51228 2598 96.21 0.187 0.187 0.185 0.1992 0.232 0.242 RANDOM 15.426
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 17.686 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 5.806 r_scangle_it 3.309 r_scbond_it 2.149 r_mcangle_it 1.248 r_angle_refined_deg 1.229 r_mcbond_it 0.805 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 17.686 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 5.806 r_scangle_it 3.309 r_scbond_it 2.149 r_mcangle_it 1.248 r_angle_refined_deg 1.229 r_mcbond_it 0.805 r_nbtor_refined 0.297 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.146 r_metal_ion_refined 0.113 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3373 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing