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The structure of nvBagel4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 293.15 0.02 M HEPES pH 8.0, 0.2 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.662 α = 75.52 b = 59.081 β = 71.2 c = 59.071 γ = 71.17
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 PILATUS3 6M 2021-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99990 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 55.17 97.4 0.044 0.053 0.028 0.997 33.7 3.4 65383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 95.5 0.066 0.079 0.043 0.99 3.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 42.64 2.28 65348 3232 97.35 0.1692 0.1683 0.1869 0.1957
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 6.403 f_angle_d 0.917 f_chiral_restr 0.06 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4896 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data scaling DIALS data reduction MOLREP phasing