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Crystal structure of ribonuclease A solved by vanadium SAD phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 20 mM sodium citrate pH 5.5, 28 % PEG 4000 with 20 mM uridine/ortho-vanadate
Crystal Properties Matthews coefficient Solvent content 2.17 43.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.51 α = 90 b = 32.66 β = 90.825 c = 72.4 γ = 90
Symmetry Space Group C 1 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 60 PIXEL DECTRIS PILATUS 12M 2019-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.26 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 41.56 100 0.088 20.6 23.6 18916 35.71
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 1.9 1.94 99.6 0.57 18.3
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 SAD FREE R-VALUE 1.9 41.56 1.34 18911 878 99.94 0.1872 0.1859 0.1871 0.2129 0.2149 46.39
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 15.9973 f_angle_d 1.1955 f_chiral_restr 0.3203 f_bond_d 0.007 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1891 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling CRANK2 phasing