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How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MZ8 PDB ENTRY 1MZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 298 0.3M phosphate buffer, 50mM NaCl, 20% PEG550 MME, 10% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.021 α = 90 b = 62.882 β = 90 c = 74.769 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 4 2004-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0 SPring-8 BL12B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 40 99.8 0.082 25.34 5.8 224307 223845 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.381 5.73 4763
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 Isomorphous to 1MZ8 THROUGHOUT PDB ENTRY 1MZ8 2 27.65 38658 37511 3023 96.9 0.188 0.188 0.1885 0.235 0.2348 RANDOM 32.8
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] -9.19 9.56 -0.37
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 7.42 c_scbond_it 5.25 c_mcangle_it 4.31 c_mcbond_it 3.32 c_angle_deg 1.3 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_scangle_it 7.42 c_scbond_it 5.25 c_mcangle_it 4.31 c_mcbond_it 3.32 c_angle_deg 1.3 c_improper_angle_d 0.84 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3328 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 12
Software Software Software Name Purpose CNS refinement DENZO data reduction CCP4 data scaling CNS phasing