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Crystal structure of the engineered quorum quenching acylase MacQ variant M1 - acylated form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 100 mM Tris-HCl, 100 mM calcium acetate, 14-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.07 α = 90 b = 80.65 β = 90.81 c = 101.6 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2022-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 53.16 98.9 0.994 11.76 3.1 64842
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.45 99.3 0.811
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.35 53.16 61599 3243 98.85 0.18734 0.18521 0.192 0.22811 0.2327 RANDOM 28.977
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] -0.04 -0.01 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.87 r_long_range_B_refined 6.521 r_long_range_B_other 6.515 r_dihedral_angle_1_deg 5.709 r_dihedral_angle_2_deg 4.987 r_scangle_other 4.368 r_mcangle_it 3.485 r_mcangle_other 3.485 r_scbond_it 2.702 r_scbond_other 2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.87 r_long_range_B_refined 6.521 r_long_range_B_other 6.515 r_dihedral_angle_1_deg 5.709 r_dihedral_angle_2_deg 4.987 r_scangle_other 4.368 r_mcangle_it 3.485 r_mcangle_other 3.485 r_scbond_it 2.702 r_scbond_other 2.702 r_mcbond_it 2.241 r_mcbond_other 2.241 r_angle_refined_deg 0.561 r_angle_other_deg 0.196 r_chiral_restr 0.029 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11369 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing