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Structure of AmiB enzymatic domain bound to the EnvC LytM domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Na Phosphate pH7.6
Crystal Properties Matthews coefficient Solvent content 4.14 70.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 237.363 α = 90 b = 237.363 β = 90 c = 237.363 γ = 90
Symmetry Space Group I 41 3 2
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 EIGER X 16M 2022-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.38 59.34 100 0.088 0.998 9.9 78.2 16294 81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.38 3.65 0.686 0.939 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 in silico model 3.381 50.005 16103 817 98.967 0.251 0.2492 0.2521 0.2909 0.2877 119.898
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 r_lrange_it 22.52 r_lrange_other 22.518 r_dihedral_angle_3_deg 18.895 r_mcangle_it 17.812 r_mcangle_other 17.809 r_scangle_other 17.101 r_scangle_it 17.076 r_dihedral_angle_6_deg 13.746 r_mcbond_it 12.02 r_mcbond_other 12.018
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.52 r_lrange_other 22.518 r_dihedral_angle_3_deg 18.895 r_mcangle_it 17.812 r_mcangle_other 17.809 r_scangle_other 17.101 r_scangle_it 17.076 r_dihedral_angle_6_deg 13.746 r_mcbond_it 12.02 r_mcbond_other 12.018 r_scbond_other 10.913 r_scbond_it 10.901 r_dihedral_angle_2_deg 8.99 r_dihedral_angle_1_deg 8.407 r_angle_refined_deg 1.405 r_angle_other_deg 0.496 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_refined 0.248 r_symmetry_nbd_other 0.197 r_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.185 r_nbd_other 0.162 r_symmetry_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.102 r_ncsr_local_group_1 0.099 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_ext_dist_refined_b 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4045 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing