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Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other T4 ENDONUCLEASE VII-HETERODUPLEX COMPLEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 25 %(w/v) PEG 3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 293K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 3.49 64.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.197 α = 90 b = 99.197 β = 90 c = 186.884 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 4 2003-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 3.1 42.27 98.9 0.066 26.8 7.9 17475 77.1
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) 3.1 3.22 95.7 0.66 3.73 7.3
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 T4 ENDONUCLEASE VII-HETERODUPLEX COMPLEX 3.1 42.27 17612 17475 703 99.2 0.258 0.258 0.2563 0.278 0.2777 RANDOM 102.7
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 2.36 c_mcangle_it 1.75 c_scbond_it 1.4 c_angle_deg 1.2 c_improper_angle_d 1.11 c_mcbond_it 1 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.6 c_scangle_it 2.36 c_mcangle_it 1.75 c_scbond_it 1.4 c_angle_deg 1.2 c_improper_angle_d 1.11 c_mcbond_it 1 c_bond_d 0.009 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 2544 Nucleic Acid Atoms 1893 Solvent Atoms 11 Heterogen Atoms 12
Software Software Software Name Purpose CNS refinement XDS data reduction XDS data scaling XSCALE data scaling PHASER phasing