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Crystal structure of nuclease MYG1(H107A) bound to Mn2+ and AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.15 M ammonium sulfate, 0.1 M MES, pH 6.0, 15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.669 α = 90 b = 96.947 β = 90 c = 115.975 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS PILATUS3 X 6M 2025-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.9786 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.31 56.58 99.9 0.99 8.8 9.2 17529 33.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.39 0.89
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 FREE R-VALUE 2.31 56.58 1.34 17476 1750 99.7 0.1964 0.1916 0.1932 0.2402 0.2402 39.12
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 5.871 f_angle_d 0.8227 f_chiral_restr 0.0487 f_plane_restr 0.0075 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2539 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction PHASER phasing