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Crystal structure of Listeria monocytogenes ChiA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8Y619-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 10% (w/v) PEG 4000, 20% (w/v) glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol, 100 mM 2-(N-morpholino) ethane sulfonic acid (MES), 100 mM imidazole
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.041 α = 94.308 b = 59.146 β = 110.69 c = 67.609 γ = 111.596
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 2022-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 1.95 45.67 93 0.123 5.1 2.6 48104
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 1.95 2 93.7 0.344 2.6
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 1.95 45.592 48104 2399 92.864 0.182 0.1798 0.1901 0.2256 0.2314 18.532
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] 2.288 0.911 -0.467 1.97 -0.83 -2.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.822 r_dihedral_angle_3_deg 12.745 r_lrange_it 9.673 r_lrange_other 9.673 r_scangle_it 8.254 r_scangle_other 8.253 r_dihedral_angle_2_deg 7.409 r_dihedral_angle_1_deg 6.29 r_scbond_it 5.929 r_scbond_other 5.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.822 r_dihedral_angle_3_deg 12.745 r_lrange_it 9.673 r_lrange_other 9.673 r_scangle_it 8.254 r_scangle_other 8.253 r_dihedral_angle_2_deg 7.409 r_dihedral_angle_1_deg 6.29 r_scbond_it 5.929 r_scbond_other 5.928 r_mcangle_other 4.713 r_mcangle_it 4.71 r_mcbond_it 3.642 r_mcbond_other 3.634 r_angle_refined_deg 1.804 r_angle_other_deg 0.601 r_nbd_refined 0.22 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.198 r_nbd_other 0.188 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.173 r_metal_ion_refined 0.125 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.082 r_gen_planes_other 0.023 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4978 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing