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Crystal structure of SPBc2 prophage-derived protein YomS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M cacodylate pH 5.5, 0.2 M ammonium nitrate, 18 % (w/v) PEG Smear Low
Crystal Properties Matthews coefficient Solvent content 2.42 49.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107 α = 90 b = 52.16 β = 95.97 c = 106.74 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 100 PIXEL DECTRIS PILATUS3 6M 2018-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 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 1.33 53.14 99.9 0.088 0.098 0.044 0.998 9.8 4.9 134241
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 1.33 1.36 100 1.397 1.564 0.693 0.498 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.33 53.14 127511 6730 99.87 0.1554 0.1542 0.1777 0.1807 RANDOM 18.458
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] -0.34 -0.05 0.32 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 11.001 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 1.898 r_angle_other_deg 1.591 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.931 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_3_deg 11.001 r_dihedral_angle_1_deg 7.004 r_angle_refined_deg 1.898 r_angle_other_deg 1.591 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4310 Nucleic Acid Atoms Solvent Atoms 851 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction CRANK2 phasing