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Structure of Csm6' from Streptococcus thermophilus in complex with cyclic hexa-adenylate (cA6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Used model obained from selenomethionine SAD phasing; model was not refined/deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.85 M sodium malonate and 5 % ethanol
Crystal Properties Matthews coefficient Solvent content 3.96 68.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.906 α = 90 b = 99.906 β = 90 c = 286.531 γ = 90
Symmetry Space Group P 43 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 80 PIXEL DECTRIS EIGER2 XE 16M 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.96 94.33 95.1 0.096 0.1 0.028 0.999 14.8 13.1 57416
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 1.96 2.2 85.8 1.352 1.405 0.382 0.78 13.3
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.96 22.34 1.34 57294 2894 54.79 0.1996 0.1976 0.1963 0.2359 0.2341
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 10.952 f_angle_d 0.87 f_chiral_restr 0.051 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6030 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 264
Software Software Software Name Purpose PHENIX refinement STARANISO data scaling autoPROC data reduction MOLREP phasing Coot model building