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Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M potassium sodium tartrate, 20-25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 3.18 61.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.823 α = 90 b = 73.012 β = 90 c = 155.229 γ = 90
Symmetry Space Group P 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 MARMOSAIC 225 mm CCD 2016-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 41.98 93.8 10.5 1 45195 37.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 69 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.104 35.537 1.79 45111 4253 93.76 0.1787 0.1768 0.1847 0.2143 0.2213 54.8646
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 15.421 f_angle_d 0.972 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3805 Nucleic Acid Atoms 630 Solvent Atoms 145 Heterogen Atoms 88
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing