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Crystallographic Structure of a Salicylate Synthase from M. abscessus (Mab-SaS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold B1MAQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 23-27% PEG 3350, 0.15-0.25M ammonium sulphate, 0.1M BIS-TRIS (pH 5.5)
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.34 α = 90 b = 94.76 β = 90 c = 102.46 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M Pt-coated cylindrical mirror 2022-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.07 56.1 100 0.186 0.195 0.057 0.997 11.9 11.4 56395
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 2.073 2.109 100 1.281 1.34 0.389 0.818 2.2 11.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.073 56.054 56394 2677 99.963 0.179 0.1769 0.2171 0.1993 33.12
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] 1.933 -2.589 0.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.348 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 6.928 r_lrange_it 6.585 r_lrange_other 6.54 r_dihedral_angle_2_deg 5.81 r_scangle_it 4.758 r_scangle_other 4.721 r_mcangle_other 3.481 r_mcangle_it 3.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.348 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 6.928 r_lrange_it 6.585 r_lrange_other 6.54 r_dihedral_angle_2_deg 5.81 r_scangle_it 4.758 r_scangle_other 4.721 r_mcangle_other 3.481 r_mcangle_it 3.478 r_scbond_it 2.969 r_scbond_other 2.936 r_mcbond_it 2.226 r_mcbond_other 2.223 r_angle_refined_deg 1.217 r_angle_other_deg 0.409 r_nbd_refined 0.201 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.149 r_nbd_other 0.14 r_symmetry_xyhbond_nbd_refined 0.113 r_symmetry_nbd_refined 0.104 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.057 r_bond_refined_d 0.005 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 6636 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing