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Structure of E. coli AmiA
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 290 See paper for details.
Crystal Properties Matthews coefficient Solvent content 2.18 43.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.515 α = 90 b = 73.899 β = 90 c = 115.563 γ = 90
Symmetry Space Group P 2 21 21
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 2021-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97950 Diamond I04-1
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 2.35 59.6 100 0.05 0.999 10.4 12.6 21955 51
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 2.35 2.43 100 0.506 0.662 1.5 12.1
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 2.35 59.586 21893 1074 99.89 0.18 0.177 0.1836 0.236 0.2372 53.965
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] -1.445 -0.646 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.701 r_dihedral_angle_6_deg 15.196 r_lrange_other 11.163 r_lrange_it 11.15 r_scangle_it 9.071 r_scangle_other 9.069 r_mcangle_it 7.151 r_mcangle_other 7.15 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.701 r_dihedral_angle_6_deg 15.196 r_lrange_other 11.163 r_lrange_it 11.15 r_scangle_it 9.071 r_scangle_other 9.069 r_mcangle_it 7.151 r_mcangle_other 7.15 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.443 r_scbond_it 6.164 r_scbond_other 6.162 r_mcbond_it 5.077 r_mcbond_other 5.06 r_angle_refined_deg 1.433 r_angle_other_deg 0.474 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.213 r_nbd_other 0.195 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.17 r_ncsr_local_group_1 0.105 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.074 r_chiral_restr 0.069 r_bond_refined_d 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 3498 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing