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Crystal structure of Thermotoga maritima endonuclease IV in the presence of cadmium and zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QTW PDB ENTRY 1QTW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 0.1 M SODIUM CHLORIDE, 0.1 M BICINE PH 9.0, 20%(V/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 550
Crystal Properties Matthews coefficient Solvent content 2.39 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.19 α = 90 b = 123.19 β = 90 c = 35.34 γ = 120
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 MARRESEARCH MX-300 2009-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
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 2.36 40.32 99.3 0.1 13.1 4.3 12749 2 10.24
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 2.36 2.44 95.6 0.17 6.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1QTW 2.36 40.32 1.36 12749 626 98.81 0.158 0.156 0.1527 0.196 0.1937 10.89
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] -0.0314 -0.0314 0.0627
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.287 f_angle_d 0.794 f_chiral_restr 0.055 f_bond_d 0.023 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2278 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing