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Crystal structure of the lasso peptide Sphingopyxin I (SpI)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M K2SO4, 20%(w/v) PEG 400
Crystal Properties Matthews coefficient Solvent content 1.59 22.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.24 α = 90 b = 39.24 β = 90 c = 31.41 γ = 120
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 PILATUS 6M-F 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.82656 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.85 50 99.8 0.067 0.997 12.01 5 24225 -3 8.602
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.85 0.9 99.6 0.689 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R-VALUE 0.85 33.98 23012 1212 99.8 0.1304 0.1292 0.1313 0.153 0.1512 RANDOM 6.914
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] 0.13 0.07 0.13 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.339 r_sphericity_free 17.628 r_dihedral_angle_3_deg 10.887 r_dihedral_angle_1_deg 7.74 r_sphericity_bonded 4.197 r_rigid_bond_restr 2.741 r_angle_refined_deg 1.813 r_angle_other_deg 1.792 r_mcangle_it 0.792 r_mcbond_it 0.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.339 r_sphericity_free 17.628 r_dihedral_angle_3_deg 10.887 r_dihedral_angle_1_deg 7.74 r_sphericity_bonded 4.197 r_rigid_bond_restr 2.741 r_angle_refined_deg 1.813 r_angle_other_deg 1.792 r_mcangle_it 0.792 r_mcbond_it 0.608 r_mcbond_other 0.592 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 310 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction XSCALE data scaling Sir2014 phasing