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The structure of nvBagel2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293.15 0.09 M HEPES sodium salt pH 7.5, 1.26 M tri-Sodium citrate, 10 %(v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 1.96 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.49 α = 90 b = 62.49 β = 90 c = 36.26 γ = 90
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 XE 16M 2019-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 1.4 44.19 86.2 0.031 0.033 0.009 1 30.2 10.2 12002
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 1.4 1.44 30 0.638 0.866 0.579 0.698 1.7
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 1.41 44.19 1.97 11969 571 87.03 0.1813 0.1783 0.1794 0.2414 0.2385
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 10.421 f_angle_d 1.209 f_chiral_restr 0.087 f_bond_d 0.012 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 604 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing