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NADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 MgCl2, HEPES and Polyacrylic acid 5100
Crystal Properties Matthews coefficient Solvent content 4.38 71.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.018 α = 90 b = 101.018 β = 90 c = 366.335 γ = 90
Symmetry Space Group P 41 21 2
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 DECTRIS EIGER2 X 16M 2022-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.4 46.67 99.81 0.08156 0.02955 0.999 14.38 14.38 75255 73.61
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 2.4 2.486 2.137 0.7324 0.456
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 2.4 46.67 1.33 75240 3632 99.83 0.2046 0.2036 0.2016 0.2242 0.2225 86.65
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 13.1498 f_angle_d 1.41 f_chiral_restr 0.0898 f_plane_restr 0.0135 f_bond_d 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5937 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 320
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing