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Crystal structure of a computationally designed colicin endonuclease and immunity pair colEdes7/Imdes7
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 8 292 12% PEG 1,500 and 0.05M MMT buffer pH=8.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.34 α = 90 b = 56.297 β = 90 c = 101.977 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 AREA DETECTOR RIGAKU 2016-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-003 1.5418
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 1.56 50.99 99.6 0.051 26.8 3.4 32715
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 1.56 1.62 97.84 0.46 6 6
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 3U43 1.6 25.51 29102 1543 99.84 0.1994 0.1972 0.2091 0.2414 0.2509 RANDOM 28.368
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] -1.87 1.14 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.099 r_dihedral_angle_4_deg 16.956 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_1_deg 6.87 r_angle_other_deg 1.26 r_angle_refined_deg 1.2 r_rigid_bond_restr 0.894 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.099 r_dihedral_angle_4_deg 16.956 r_dihedral_angle_3_deg 12.175 r_dihedral_angle_1_deg 6.87 r_angle_other_deg 1.26 r_angle_refined_deg 1.2 r_rigid_bond_restr 0.894 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling PHASER phasing