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Crystal structure of a double glycine motif protease from AMS/PCAT transporter in complex with the leader peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 282 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.0 2M N-acetyl-D-glucosamine, 0.05 M Tris and BICINE pH 8.5, 20% v/v polyethylene glycol 500 monomethyl ether, 10% w/v polyethylene glycol 20000, and 8% v/v formamide
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.888 α = 90 b = 119.426 β = 93.84 c = 76.522 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 80 CCD RAYONIX MX-300 2018-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.98 76.4 99.8 9.3 5.1 47187
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 1.985
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 THROUGHOUT 2 50.01 43389 2306 99.8 0.23606 0.23434 0.2445 0.26829 0.276 RANDOM 37.026
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] -2.16 0.47 -4.37 6.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 21.581 r_dihedral_angle_3_deg 17.864 r_dihedral_angle_1_deg 7.612 r_long_range_B_refined 7.414 r_long_range_B_other 7.414 r_scangle_other 5.392 r_mcangle_it 4.392 r_mcangle_other 4.391 r_scbond_it 3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 21.581 r_dihedral_angle_3_deg 17.864 r_dihedral_angle_1_deg 7.612 r_long_range_B_refined 7.414 r_long_range_B_other 7.414 r_scangle_other 5.392 r_mcangle_it 4.392 r_mcangle_other 4.391 r_scbond_it 3.54 r_scbond_other 3.539 r_mcbond_it 2.99 r_mcbond_other 2.989 r_angle_refined_deg 1.815 r_angle_other_deg 1.033 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4843 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data scaling AutoSol phasing PHENIX model building