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NADase from Aspergillus fumigatus with trapped reaction products
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YGE D_1292105770
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.04 M Potassium phosphate monobasic, 16% PEG 8000 and 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.815 α = 90 b = 63.815 β = 90 c = 257.723 γ = 120
Symmetry Space Group P 32 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 DECTRIS PILATUS 6M-F 2018-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 85.9 99.74 0.02465 0.999 15.17 2 68236 27.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 0.644 0.477 1.04
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292105770 1.7 85.9 1.34 68230 3387 99.75 0.1708 0.1692 0.2013 0.1922 35.24
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 17.9506 f_angle_d 0.8805 f_chiral_restr 0.0553 f_bond_d 0.0068 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3302 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 263
Software Software Software Name Purpose PHENIX refinement XDS data processing Aimless data scaling PHASER phasing Coot model building XDS data reduction