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Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA, Mg2+ and Mn2+ ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 279 PEG10000, NaCl, magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.73 54.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.582 α = 90 b = 98.582 β = 90 c = 119.619 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2015-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.91376 ESRF ID29
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 2.6 49.291 99.9 0.131 6.5 19.8 21142 1.9
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 2.6 2.69 99.4 0.567 1.9 15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CO8 2.602 49.291 1.34 21111 1084 99.97 0.214 0.212 0.2227 0.2523 0.2586 Random selection
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 19.692 f_angle_d 0.874 f_chiral_restr 0.034 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3071 Nucleic Acid Atoms 595 Solvent Atoms 66 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction PHENIX phasing iMOSFLM data reduction