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Crystal structure of the ATPase domain from bacterial mismatch repair endonuclease Aquifex aeolicus MutL.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 50 mM Bis-Tris
1.5 M sodium chloride
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.84 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.929 α = 90 b = 145.253 β = 90 c = 176.769 γ = 90
Symmetry Space Group I 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 CCD RAYONIX MX-225 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.44 43.05 100 0.134 0.054 16.3 7.2 21839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.44 3.57 100 1.008 0.397 0.725 2.13 7.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BKN 3.443 43.05 20395 1869 92.79 0.2597 0.2561 0.2538 0.2954 0.2913
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 f_dihedral_angle_d 13.714 f_angle_d 0.587 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6108 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PHENIX model building HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing