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Crystal structure of Janthinobacterium lividum PE-like toxin, Jlx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294.16 0.1 M Amino acids, 0.1 M Buffer System 1 pH 6.5, 30 % v/v Precipitant Mix 1 (condition H1 of the Morpheus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.86 57.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.625 α = 90 b = 143.241 β = 119.351 c = 110.67 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 EIGER2 XE 16M 2021-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9793 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 115.6 94.6 0.103 0.028 1 12.5 14.1 186952
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 1.75 1.95 71.3 2.07 2.15 0.558 0.722 1.2 14.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 115.6 186950 9406 61.065 0.215 0.2134 0.2092 0.2475 0.2434 31.048
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] -0.079 0.025 -0.467 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_dihedral_angle_4_deg 15.588 r_dihedral_angle_3_deg 12.85 r_dihedral_angle_1_deg 6.891 r_lrange_it 5.435 r_lrange_other 5.392 r_scangle_it 3.604 r_scangle_other 3.604 r_mcangle_it 3.223 r_mcangle_other 3.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.558 r_dihedral_angle_4_deg 15.588 r_dihedral_angle_3_deg 12.85 r_dihedral_angle_1_deg 6.891 r_lrange_it 5.435 r_lrange_other 5.392 r_scangle_it 3.604 r_scangle_other 3.604 r_mcangle_it 3.223 r_mcangle_other 3.223 r_scbond_it 2.199 r_scbond_other 2.196 r_mcbond_it 1.973 r_mcbond_other 1.972 r_angle_refined_deg 1.353 r_angle_other_deg 1.229 r_nbd_other 0.336 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.2 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_other 0.08 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19000 Nucleic Acid Atoms Solvent Atoms 1573 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement DIALS data reduction STARANISO data scaling PHASER phasing